Use of a polypeptide for detecting, preventing or treating a pathological condition associated with a degenerative, neurological or autoimmune disease

ABSTRACT

The invention concerns the use of at least one polypeptide comprising a protein fragment to obtain a diagnostic, prognostic, prophylactic or therapeutic composition for detecting, preventing or treating a pathological condition associated with a degenerative and/or neurological and/or autoimmune disease, said protein being selected among the proteins whereof the peptide sequence in native state corresponds to SEQ ID No 1, SEQ ID No 2, SEQ ID No 3, SEQ ID No 4, SEQ ID No 5, SEQ ID No 6, SEQ ID No 7, SEQ ID No 8, SEQ ID No 9, SEQ ID No 10, SEQ ID No 11, SEQ ID No 12, SEQ ID No 13, SEQ ID No 14, SEQ ID No 15, SEQ ID No 16, SEQ ID No 17, SEQ ID No 18, SEQ ID No 19, SEQ ID No 20, SEQ ID No 21, SEQ ID No 22, SEQ ID No 23, SEQ ID No 24, SEQ ID No 25, SEQ ID No 26, SEQ ID No 27, SEQ ID No 28, and SEQ ID No 29, and the peptide sequences having at least 70% identity, preferably at least 80% identity and advantageously at least 98% identity with any one of the peptide sequences SEQ ID No 1 to SEQ ID No 8 and SEQ ID No 10 to SEQ ID No 29, and the peptide sequences or fragments of said sequences belonging to a common family of proteins selected among perlecan, the precursor of the retinol-binding plasmatic protein, of the GM2 activator protein, of calgranulin B and of saponin B.

BACKGROUND

The present invention relates in particular to the use of at least onepolypeptide to obtain a diagnostic, prognostic, prophylactic ortherapeutic composition for for detecting, preventing or treating apathological condition associated with a degenerative and/or autoimmuneand/or neurological disease.

According to the invention, the expression degenerative disease isunderstood to mean a disease in which a process of cell death or of celldestruction is associated with physiological and/or clinical disorders.Alzheimer's disease, amyotrophic lateral sclerosis and Parkinson'sdisease are classified amongst neurogenerative diseases. The expressionautoimmune disease is understood to mean a hyperactivity of the immunesystem toward one or more autoantigens. Multiple sclerosis (MS),rheumatoid arthritis (RA) and lupus erythematosus are classified amongautoimmune diseases.

Multiple sclerosis is a chronic disease of the central nervous system inhumans which progresses through a succession of phases of remission andof flare-up or in a regular progression and whose anatomicopathologicalcharacteristic consists in the formation of well delimited demyelinationzones in the white substance of the brain and of the spinal cord.

At the histological level, these zones exhibit, at the early stage ofthe lesional process, a degradation of the periaxonal myelin associatedwith an impairment of the glial cells responsible for thisdemyelination.

Inflammatory macrophage activation causing the microglial cells(resident tissue macrophages of the central nervous system), as well as,probably, macrophages from infiltrated blood monocytes, is associatedwith this demyelination process and contributes to the destruction ofthe myelinated sheets. At the center of the demyelinated zone, there isa relative depletion of glial cells whereas a proliferation ofastrocytes develops at the periphery and can invade the demyelinatedplaque in order to generate a fibrous or gliotic plaque. These scleroticstructures are responsible for the name given to the disease.

Another characteristic of these plaques is their almost systematicassociation with a vascular element around which they develop.

At the histological level, a frequent alteration of the blood-brainbarrier (BBB) consisting of capillary endothelium is observed. One ofthe key elements in maintaining the BBB consists of the underlyingpresence of cytoplasmic extensions of the astrocytes, called astrocyticfeet. Possibly, the astrocytic feet induce the formation or allow themaintenance of tight joining structures which ensure the cohesion of thecapillary endothelial barrier concretizing the BBB. However, variouspathological models report the alteration of the BBB and a depletion ofthe astrocytic feet.

Moreover, in the lesional process in MS, the alteration of the BBBcontributes toward amplifying the associated inflammatory response bythe influx of lymphoid cells from the bloodstream. The contribution ofthe inflammation associated with the immune cells is important in MS andparticipates in the lesional process.

The etiology of MS is the source of a current debate because the diseasecould have various origins. Hypotheses have been emitted on a bacterialand/or viral origin. Moreover, as described in patent application WO95/21859, H. Perron et al. have been led to investigate one or moreeffector agents for the pathogenic process resulting in the typicalformation of demyelination plaques and in astrocytic gliosis. In thecontext of this study, they demonstrated the presence, in thecerebrospinal fluid (CSF) and the serum of MS patients, of at least onefactor which exhibits a toxic activity toward human or animal astrocyteand oligodendrocyte cells. This toxic activity is characterized by acytomorphological disorganization of the network of intermediatefilaments and/or a degradation of the proteins of said filaments and/ora cell death by apoptosis of the glial cells. They established asignificant correlation between the in vitro detection of this toxicactivity in samples of CSF and of serum of MS patients and multiplesclerosis by a quantitative calorimetric assay with methyltetrazoliumbromide (MTT) of the live cells, as described in patent application WO95/21859. Moreover, C. Malcus-Vocanson et al. have shown that urine is avery favorable biological fluid for the detection of the activity ofthis toxic factor and developed a method using flow cytometry to detectand/or quantify the adherent glial cells which are dead throughapoptosis. All the information relating to this method is described inpatent application WO 98/11439, whose content is incorporated by way ofreference.

Trials were carried out starting with a protein fraction of CSF and ofurine from MS patients in order to try to identify this toxic factor.The protein content of each fraction was separated on a 12% SDS-PAGE geland observed after silver staining of the gel. Among the proteinsobserved, a protein fraction centered over an apparent molecular weightof about 21 kD was found not predominantly associated with the toxicactivity detected in vitro and a fraction centered over an apparentmolecular weight of about 17 kD was found predominantly associated withthe toxic activity.

Injection of the fraction from the SCF of MS patients into the brain ofLewis rats and postmortem histological observation of brain sections ofthe rats made it possible to observe, three months after the injection,an apoptosis of the astrocytic population and the formation ofdemyelination plaques. All the information is contained in patentapplication WO 97/33466, whose content is incorporated by way ofreference. These observations are in accordance with those which havebeen made on the brain sections of patients suffering from MS, afterbiopsy (N. Benjelloun et al. Cell. Mol. Biol., 1998, 44(4), 579–583).

SUMMARY

The present inventors have now identified and analyzed the proteinsassociated with this toxic activity toward glial cells in biologicalsamples from MS patients, in particular in urine, cerebrospinal fluidand serum.

After purification of the proteins and separation on SDS-TRICINE gel,the inventors have demonstrated the presence of four bands of interesthaving different apparent molecular weights, of 8, 14, 18 and 20 kDrespectively, corresponding to at least five different protein families.The proteins of these families were then analyzed by mass spectrometryand/or sequencing and a search for homology in data banks (NCBI, BasicBlast Search, Protein Blastp, the protein sequences are entered in aFASTA format into the nr database, the algorithm used is MatrixBLOSUM62, the identity called “Identities” corresponds to the number ofidentical amino acids, given as a percentage, and the positivity“Positives” corresponds to the amino acids exhibiting biologicalequivalence according to the abovementioned parameters of the software,given as a percentage). These proteins belong to the protein families ofPerlecan, of the precursor of the retinol-binding plasma protein, of theGM2 activator protein, of calgranulin and of saposin B. More precisely,the proteins are (i) for the 20 kD band, the C-terminal fragment ofPerlecan which starts at amino acid 3464 and ends at amino acid 3707(Murdoch A D et al. J Biol Chem, 1992, April 25; 267 (12):8544–47), anddesignated by a reference in the sequence identifier SEQ ID No. 2 (thefull-length Perlecan protein being designated by a reference in SEQ IDNo. 1), (ii) for the 20 kD band, the precursor of the retinol-bindingplasma protein (Monaco H L et al., Science, 1995, 268 (5213):1039–1041)whose sequence is given in SEQ ID No. 4, (iii) for the 18 kD band, theGM2 activator protein (Furst W et al., Euro J Biochem, 1990, Sep. 24;193(3):709–14) identified in SEQ ID No. 8, (iv) for the 14 kD band,calgranulin B (Lagasse. E et al., Mol Cell Biol, 1988, Jun.;8(6):2402–10) identified in SEQ ID No. 17 and (v) for the 8 kD band,saposin B (Kleinschmidt T et al., Biol Chem Hoppe Seyler, 1988,December; 369(12):1361–5) represented in SEQ ID No. 24. They have alsodemonstrated the presence of variant sequences to said referencesequences, in particular for the 18 kD band a variant sequence of theGM2 activator protein designated by the reference SEQ ID No. 9. Thesevariant protein sequences are the product of mutations at the level ofthe genes encoding said proteins or are the result of splicingphenomena. It should be noted, for example, that calprotectin is avariant of calgranulin B.

The C-terminal fragment of the Perlecan protein (SEQ ID No. 2) isencoded, for example, by the DNA nucleotide sequence SEQ ID No. 69,taking into account the genetic code. The precursor protein for theretinol-binding plasma protein (SEQ ID No. 4) is encoded, for example,by the DNA nucleotide sequence SEQ ID No. 70, taking into account thegenetic code. The GM2 activator protein (SEQ ID No. 8) is encoded, forexample, by the DNA nucleotide sequence SEQ ID No. 31, taking intoaccount the genetic code. The peptides FSWDNCFEGK DPAVIR and YSLPKSEFAVPDLELP derived from the GM2 activator mutated polypeptide (SEQ ID No. 9)are encoded by the DNA nucleotide sequences SEQ ID No. 66 and SEQ ID No.67, respectively, taking into account the genetic code. The calgranulinB protein (SEQ ID No. 17) is encoded, for example, by the DNA nucleotidesequence SEQ ID No. 42, taking into account the genetic code. Thesaposin B protein (SEQ ID No. 24) is encoded, for example, by the DNAnucleotide sequence SEQ ID No. 53, taking into account the genetic code.

The expression protein family is understood to mean all the proteinsencoded from the same DNA gene and which result from a differentialmultiple splicing of the gene and/or of a different reading frame. TheDNA gene is transcribed with alternative splicing phenomena, leading tothe translation of different primary sequences of proteins. All theseproteins belong to the same protein family. The term “protein family”also includes proteins which exhibit at least 70% identity, preferablyat least 80% identity and advantageously at least 98% identity with areference protein sequence of the family.

The expression multiple splicing is understood to mean a splicingoccurring at least once in the nucleotide region of interest.

For example, the expression precursor protein family for theretinol-binding plasma protein designates the protein family comprisingat least the proteins or fragments of proteins having the sequence SEQID No. 4, SEQ ID No. 5, SEQ ID No. 6, SEQ ID No. 7, and the proteinsencoded by the corresponding gene according to different reading frames.

For example, the expression GM2 activator protein family designates theprotein family comprising at least the proteins or fragments of proteinshaving the sequence SEQ ID No. 8, SEQ ID No. 9, SEQ ID No. 10, SEQ IDNo. 11, SEQ ID No. 12, SEQ ID No. 13, SEQ ID No. 14, SEQ ID No. 15, SEQID No. 16, and the proteins encoded by the corresponding gene accordingto different reading frames, which result from a differential multiplesplicing of the gene and/or of a different reading frame.

For example, the expression calgranulin B protein family designates theprotein family comprising at least the proteins or fragments of proteinshaving the sequence SEQ ID No. 17, SEQ ID No. 18, SEQ ID No. 19, SEQ IDNo. 20, SEQ ID No. 21, SEQ ID No. 22, SEQ ID No. 23, and the proteinsencoded by the corresponding gene according to different reading frames,which result from a differential multiple splicing of the gene and/or ofa different reading frame. The proteins MRP14 (SEQ ID No. 17) and MRP8(SEQ ID No. 18) have a different protein sequence while being encoded bythe same gene; they belong to the same protein family.

For example, the expression saposin B protein family designates theprotein family comprising at least the proteins or fragments of proteinshaving the sequence SEQ ID No. 24, SEQ ID No. 25, SEQ ID No. 26, SEQ IDNo. 27, SEQ ID No. 28, SEQ ID No. 29, and the proteins encoded by thecorresponding gene according to different reading frames, which resultfrom a differential multiple splicing of the gene and/or of a differentreading frame.

The expression nucleic acid family encoding a protein is understood tomean all the cDNA and/or RNA nucleic sequences transcribed from the sameDNA gene and which result from a differential multiple splicing. The DNAgene is transcribed with differential splicing phenomena and leads tothe synthesis of different nucleic acids (cDNA, RNA) of differentsequences. All these cDNA and mRNA sequences are considered to belong tothe same nucleic acid family.

For example, the expression nucleic acid family encoding the precursorprotein family for the retinol-binding plasma protein designates thenucleic acid family comprising at least the nucleic acids or fragmentshaving the sequence SEQ ID No. 30.

For example, the expression nucleic acid family encoding the GM2activator protein family designates the nucleic acid family comprisingat least the nucleic acids or fragments having the sequences SEQ ID No.31, SEQ ID No. 32, SEQ ID No. 33, SEQ ID No. 34, SEQ ID No. 35, SEQ IDNo. 36, SEQ ID No. 37, SEQ ID No. 38, SEQ ID No. 39, SEQ ID No. 40, SEQID No. 41 which result from a differential multiple splicing of the geneand/or of a different reading frame.

For example, the expression nucleic acid family encoding the calgranulinB protein family designates the nucleic acid family comprising at leastthe nucleic acids or fragments having the sequences SEQ ID No. 42, SEQID No. 43, SEQ ID No. 44, SEQ ID No. 45, SEQ ID No. 46, SEQ ID No. 47,SEQ ID No. 48, SEQ ID No. 49, SEQ ID No. 50, SEQ ID No. 51, SEQ ID No.52 which result from a differential multiple splicing of the gene and/orof a different reading frame.

For example, the expression nucleic acid family encoding the saposin Bprotein family designates the nucleic acid family comprising at leastthe nucleic acids or fragments having the sequences SEQ ID No. 53, SEQID No. 54, SEQ ID No. 55 which result from a differential multiplesplicing of the gene and/or of a different reading frame.

The expression “splicing” is understood to mean a mechanism of excisionof the introns and of joining of the exons during the maturation of thetranscripts and the expression “differential splicing” is understood tomean the existence of several schemes for splicing of a primarytranscript resulting in the formation of different messenger RNAs andcapable of leading to the synthesis of several different proteins(Kaplan and Delpech, Biologie Moléculaire et Médecine, 1993, 2^(nd)edition, Médecine et Sciences, Flammarion, pages 73–77). This phenomenonis widely described in the scientific literature. By way of example,there may be mentioned the model of the genes which encode the heavy andlight immunoglobulin chains, the model of the gene for dystrophin, themodel of the gene for alpha-amylase, the gene for myelin, and the like.

It is known that the eukaryotic genes in particular comprise regions(exons) which encode fragments of the protein encoded by said gene andother regions (introns) which do not have a protein equivalent. This isdue to the fact that the genes are first transcribed to a “primary” RNAwhich is then cut by splicing enzymes at the level of specificnucleotide sites (splicing sites). These enzymes then join the regionsencoding the protein, thus reconstituting a “secondary” RNA from whichthe intron regions have been removed. Moreover, depending on thecellular phenotypes (and therefore the tissues or the differentiation),these enzymes are not all expressed, and thus the same RNA may bedifferently spliced in the cells of the same individual, thus generatingproteins with differences in sequence. However, these phenomena may alsobe applied to nucleotide regions which are completely coding (exons),but which, according to different possible splicings, will generateseveral different proteins from the same nucleotide region by thephenomenon of differential splicing between the different proteinproducts.

Furthermore, it is known that nucleotide regions may have severalreading frames according to the three potential frames of the geneticcode. Thus, the presence of several initiation codons for translation inseveral reading frames and/or a splicing of primary RNA joiningnucleotide sequences present in different reading frames on the DNA,allows the same DNA region to generate protein products with no mutualrelationship from the point of view of the peptide sequence.

Finally, the genetic polymorphism existing between individuals of thesame species and/or individual mutations can create or eliminatesplicing sites from a given DNA region, and thus modify the sequence andthe structure of the protein product(s) normally produced by thisregion.

Thus, the combination of these different phenomena can allow the samenucleotide sequence corresponding to a DNA segment, identified asdetermining a genetic region of interest in a given study, to comprisethe information which is necessary and sufficient to define a wholefamily of RNA spliced according to different and alternative schemes, invarious reading frames and, thereby obviously, proteins and polypeptideshaving “mosaic” sequences according to one reading frame or evenaccording to the three potential frames and mutations possibly linked togenetic polymorphism.

An example of this phenomenon may be represented by the nucleotideregion of the HIV-1 retrovirus env gene. Indeed, several differentproteins are encoded by segments of the same sequence: for example, theenvelope glycoprotein, and the regulatory proteins TAT, REV, NEF, VIF.

It is also known that proteins may result from the assembly of identicalsubunits (homodimers, homomultimers) or different subunits(heterodimers, heteromultimers). Thus, the various protein productsencoded by the same DNA region may also assemble with each other toconstitute multimeric complex protein entities. This phenomenon is inaddition to the preceding ones and, when a protein is identified by apeptide fragment, it is possible to logically identify all the otherconstituent elements of this complex protein and the spliced RNA and DNAsegments encoding them, as well as all the members of the family ofprotein products and their assemblies. Another example is provided bythe human DNA region encoding the family of MRP14, calgranulin B, MRP8,calprotectin and psoriasin proteins, and the like.

Accordingly, the subject of the present invention is the use of at leastone polypeptide comprising at least one fragment of a protein to obtaina diagnostic, prognostic, prophylactic or therapeutic composition fordetecting, prognosticating, preventing or treating a pathologicalcondition associated with a degenerative and/or autoimmune disease, saidprotein being chosen from proteins whose peptide sequence in the nativestate corresponds to SEQ ID No. 1, SEQ ID No. 2, SEQ ID No. 3, SEQ IDNo. 4, SEQ ID No. 5, SEQ ID No. 6, SEQ ID No. 7, SEQ ID No. 8, SEQ IDNo. 10, SEQ ID No. 11, SEQ ID No. 12, SEQ ID No. 13, SEQ ID No. 14, SEQID No. 15, SEQ ID No. 16, SEQ ID No. 17, SEQ ID No. 18, SEQ ID No. 19,SEQ ID No. 20, SEQ ID No. 21, SEQ ID No. 22, SEQ ID No. 23, SEQ ID No.24, SEQ ID No. 25, SEQ ID No. 26, SEQ ID No. 27, SEQ ID No. 28 and SEQID No. 29 and the peptide sequences which exhibit at least 70% identity,preferably at least 80% identity and advantageously at least 98%identity with any of the abovementioned peptide sequences, and thepeptide sequences or the fragments of said sequences belonging to thesame family of proteins chosen from Perlecan, the precursor of theretinol-binding plasma protein, GM2 activator protein, calgranulin B andsaposin B. In specific embodiments, at least two abovementionedpolypeptides are used in combination in order to obtain a diagnostic,prognostic, prophylactic or therapeutic composition for detecting,prognosticating, preventing or treating a pathological conditionassociated with a degenerative and/or autoimmune disease.

The invention also relates to the use of at least one polypeptidecomprising at least one fragment of a protein to obtain a diagnostic,prognostic, prophylactic or therapeutic composition for detecting,prognosticating, preventing or treating a pathological conditionassociated with a degenerative and/or autoimmune disease, said proteinbeing chosen from the proteins whose peptide sequence in the nativestate corresponds to SEQ ID No. 2, SEQ ID No. 4, SEQ ID No. 8, SEQ IDNo. 17 and SEQ ID No. 24 and the peptide sequences which exhibit atleast 70% identity, preferably at least 80% identity and advantageouslyat least 98% identity with any one of the abovementioned peptidesequences. Advantageously, the five polypeptides which correspond to theabove definition are used in combination.

Preferably, the peptide sequence of said polypeptide comprises, orconsists of, a sequence chosen from any one of SEQ ID No. 2, SEQ ID No.4, SEQ ID No. 8, SEQ ID No. 17 and SEQ ID No. 24.

The invention also relates to the use of at least one fragment of one ofthe abovementioned polypeptides for the preparation of an immunogenicpeptide, said peptide comprising all or part of at least one of thesequences designated by the references SEQ ID Nos. 58 to 65 and beingused for the production of monoclonal antibodies.

The subject of the invention is also the use of at least one nucleotidefragment to obtain a diagnostic, prognostic, prophylactic or therapeuticcomposition for detecting, prognosticating, preventing or treating apathological condition associated with a degenerative and/or autoimmunedisease, according to which said nucleotide fragment is chosen fromfragments which encode at least one fragment of a protein, said proteinbeing chosen from proteins whose peptide sequence in the native statecorresponds to SEQ ID No. 1, SEQ ID No. 2, SEQ ID No. 3, SEQ ID No. 4,SEQ ID No. 5, SEQ ID No. 6, SEQ ID No. 7, SEQ ID No. 8, SEQ ID No. 10,SEQ ID No. 11, SEQ ID No. 12, SEQ ID No. 13, SEQ ID No. 14, SEQ ID No.15, SEQ ID No. 16, SEQ ID No. 17, SEQ ID No. 18, SEQ ID No. 19, SEQ IDNo. 20, SEQ ID No. 21, SEQ ID No. 22, SEQ ID No. 23, SEQ ID No. 24, SEQID No. 25, SEQ ID No. 26, SEQ ID No. 27, SEQ ID No. 28 and SEQ ID No. 29and the peptide sequences which exhibit at least 70% identity,preferably at least 80% and advantageously at least 98% identity withany one of the above peptide sequences, and the fragments complementaryto said fragments, and the peptide sequences or the fragments of saidsequences belonging to the same family of proteins chosen from Perlecan,the precursor of the retinol-binding plasma protein, GM2 activatorprotein, calgranulin B and saposin B. It is within the capability ofpersons skilled in the art to determine the nucleic sequences of thenucleotide fragments from the peptide sequences and the genetic code,this forming part of their general knowledge.

Preferably, said nucleotide fragment encodes a protein which, in thenative state, consists of a sequence chosen from any one of thesequences SEQ ID Nos. 1 to 8 and SEQ ID Nos. 10 to 29 cited above, andamong the peptide sequences or the fragments of said sequences belongingto the same family of proteins chosen from Perlecan, the precursor ofthe retinol-binding plasma protein, GM2 activator protein, calgranulin Band saposin B.

Another subject of the invention is the use of at least one nucleotidefragment to obtain a diagnostic, prognostic, prophylactic or therapeuticcomposition for detecting, prognosticating, preventing or treating apathological condition associated with a degenerative and/orneurological and/or autoimmune disease according to which said fragmentis a fragment of a nucleic sequence chosen from any one of SEQ ID No.30, SEQ ID No. 31, SEQ ID No. 32, SEQ ID No. 33, SEQ ID No. 34, SEQ IDNo. 35, SEQ ID No. 36, SEQ ID No. 37, SEQ ID No. 38, SEQ ID No. 39, SEQID No. 40, SEQ ID No. 41, SEQ ID No. 42, SEQ ID No. 43, SEQ ID No. 44,SEQ ID No. 45, SEQ ID No. 46 and SEQ ID No. 47, SEQ ID No. 48, SEQ IDNo. 49 and SEQ ID No. 50, SEQ ID No. 51, SEQ ID No. 52, SEQ ID No. 53,SEQ ID No. 54, SEQ ID No. 55, SEQ ID No. 56, SEQ ID No. 57, SEQ ID No.67, SEQ ID No. 66, SEQ ID No. 69, SEQ ID No. 70 and SEQ ID No. 71, andtheir complementary sequences.

The invention also relates to the use of a ligand specific for apolypeptide or for a nucleotide fragment as defined above to obtain adiagnostic, prognostic, prophylactic or therapeutic composition fordetecting, prognosticating, preventing or treating a pathologicalcondition associated with a degenerative and/or autoimmune disease.

The expression ligand is understood to mean any molecule capable ofcombining with a polypeptide, such as a monoclonal antibody, apolyclonal antibody, a receptor, a substrate with enzymatic activity, oran enzyme for which said polypeptide is a cofactor. The production ofpolyclonal or monoclonal antibodies forms part of the general knowledgeof persons skilled in the art. There may be mentioned, by way ofreference, Köhler G. and Milstein C. (1975): Continuous culture of fusedcells secreting antibody of predefined specificity, Nature 256:495–497and Galfre G. et al. (1977) Nature, 266:522–550 for the production ofmonoclonal antibodies and Roda A., Bolelli G. F.: Production ofhigh-titer antibody to bile acids, Journal of Steroid Biochemistry, Vol.13, pp. 449–454 (1980) for the production of polyclonal antibodies.

The expression ligand is also understood to mean any molecule capable ofcombining with a nucleotide fragment, such as a partially or completelycomplementary nucleotide fragment, a complementary polynucleotide, or ananti-nucleic acid antibody. The production of nucleotide fragments or ofpolynucleotides forms part of the general knowledge of persons skilledin the art. There may be mentioned in particular the use of restrictionenzymes, and chemical synthesis on an automated synthesizer, for exampleon synthesizers marketed by the company Applied Biosystem. Moreover,techniques for the production of anti-nucleic acid antibodies are known.There may be mentioned, by way of examples, Philippe Cros et al.,Nucleic Acides Researc, 1994, Vol. 22, No. 15, 2951–2957; Anderson, W.F. et al. (1988) Bioessays, 8(2), 69–74; Lee, J. S. et al. (1984) FEBSLett., 168, 303–306; Malfoy, B. et al. (1982) Biochemistry, 21(22),5463–5467; Stollar, B. D. et al., J. J. (eds) Methods in Enzymology,Academic Press, pp. 70–85; Traincard, F. et al. (1989) J. Immunol.Meth., 123, 83–91 and Traincard, F. et al. (1989) Mol. Cell. Probes, 3,27–38).

The subject of the invention is also a method for detecting at least oneprotein associated with a degenerative and/or autoimmune disease in abiological sample in which the biological sample is brought into contactwith at least one ligand specific for at least one polypeptide, saidpolypeptide comprising at least one fragment of a protein and saidprotein being chosen from the proteins whose peptide sequence in thenative state corresponds to SEQ ID No. 1, SEQ ID No. 2, SEQ ID No. 3,SEQ ID No. 4, SEQ ID No. 5, SEQ ID No. 6, SEQ ID No. 7, SEQ ID No. 8,SEQ ID No. 10, SEQ ID No. 11, SEQ ID No. 12, SEQ ID No. 13, SEQ ID No.14, SEQ ID No. 15, SEQ ID No. 16, SEQ ID No. 17, SEQ ID No. 18, SEQ IDNo. 19, SEQ ID No. 20, SEQ ID No. 21, SEQ ID No. 22, SEQ ID No. 23, SEQID No. 24, SEQ ID No. 25, SEQ ID No. 26, SEQ ID No. 27, SEQ ID No. 28and SEQ ID No. 29 and the peptide sequences which exhibit at least 70%identity, preferably at least 80% identity and advantageously at least98% identity with any one of the peptide sequences SEQ ID No. 1 to SEQID No. 8 and SEQ ID No. 10 to 29, and the peptide sequences or fragmentsof said sequences belonging to the same family of proteins chosen fromPerlecan, the precursor of the retinol-binding plasma protein, GM2activator protein, calgranulin B and saposin B, and then the formationof a complex between said polypeptide and said ligand is detected. Saidligand is advantageously a monoclonal antibody, a polyclonal antibody, areceptor, a substrate with enzymatic activity or an enzyme for whichsaid polypeptide is a cofactor.

Likewise, the invention relates to a method for detecting at least oneligand associated with a degenerative and/or autoimmune disease, in abiological sample, characterized in that the biological sample isbrought into contact with at least one polypeptide comprising at leastone fragment of a protein, said protein being chosen from the proteinswhose peptide sequence in the native state corresponds to SEQ ID No. 1,SEQ ID No. 2, SEQ ID No. 3, SEQ ID No. 4, SEQ ID No. 5, SEQ ID No. 6,SEQ ID No. 7, SEQ ID No. 8, SEQ ID No. 10, SEQ ID No. 11, SEQ ID No. 12,SEQ ID No. 13, SEQ ID No. 14, SEQ ID No. 15, SEQ ID No. 16, SEQ ID No.17, SEQ ID No. 18, SEQ ID No. 19, SEQ ID No. 20, SEQ ID No. 21, SEQ IDNo. 22, SEQ ID No. 23, SEQ ID No. 24, SEQ ID No. 25, SEQ ID No. 26, SEQID No. 27, SEQ ID No. 28 and SEQ ID No. 29 and the peptide sequenceswhich exhibit at least 70% identity, preferably at least 80% identityand advantageously at least 98% identity with any one of the peptidesequences SEQ ID No. 1 to SEQ ID No. 8 and SEQ ID Nos. 10 to SEQ ID No.29, and the peptide sequences or the fragments of said sequencesbelonging to the same family of proteins chosen from Perlecan, theprecursor of the retinol-binding plasma protein, GM2 activator protein,calgranulin B and saposin B, and then the formation of a complex betweensaid polypeptide and said ligand is detected. The ligand is any moleculewhich satisfies the conditions previously described.

Preferably, in the methods described above, the sequence of thepolypeptide comprises or consists of a peptide sequence chosen from anyone of SEQ ID No. 1 to 8 and SEQ ID No. 10 to 29 above and the peptidesequences or the fragments of said sequences belonging to the samefamily of proteins chosen from Perlecan, the precursor of theretinol-binding plasma protein, GM2 activator protein, calgranulin B andsaposin B.

The invention also relates to a novel polypeptide which comprises atleast one fragment of a protein whose peptide sequence corresponds toSEQ ID No. 9, said fragment exhibiting at least one mutation, inparticular at least two mutations, in relation to the reference sequenceSEQ ID No. 8. The polypeptide is advantageously chosen from thepolypeptides which comprise the amino acid sequence FSWDNCFEGKDPAVIR,designated by the reference SEQ ID No. 68, and the amino acid sequenceYSLPKSEFAVPDLELP, designated by the reference SEQ ID No. 72.

In particular, said polypeptide comprises or consists of SEQ ID No. 9.This polypeptide is used to obtain a diagnostic, prognostic,prophylactic or therapeutic composition for detecting, prognosticating,preventing or treating a pathological condition associated with adegenerative and/or autoimmune disease, alone or as a mixture with atleast one polypeptide as defined above.

One of the subjects of the invention is also a nucleotide fragment whichencodes the fragment of the protein whose peptide sequence correspondsto SEQ ID No. 9, said fragment of said protein exhibiting at least onemutation, in particular two mutations relative to the reference sequenceSEQ ID No. 8. Said nucleotide fragment in particular comprises orconsists of a fragment which encodes SEQ ID No. 9. This fragment is usedto obtain a diagnostic, prognostic, prophylactic or therapeuticcomposition for detecting, preventing or treating a pathologicalcondition associated with a degenerative and/or autoimmune disease,alone or as a mixture with at least one nucleotide fragment as definedabove.

The subject of the invention is also a method for detecting at least oneligand associated with a degenerative and/or autoimmune disease, in abiological sample, according to which the biological sample is broughtinto contact with at least the polypeptide which comprises or consistsof SEQ ID No. 9 or a mixture of polypeptides comprising this polypeptideand at least one polypeptide as described above, and then the formationof a complex or of complexes between the polypeptide(s) and thecorresponding ligand(s) is detected; it is to be understood that theexpression ligand is understood to mean a molecule which satisfies theabovementioned conditions.

The invention also relates to a method for detecting at least thereference polypeptide SEQ ID No. 9 or a fragment of said polypeptide,this fragment comprising at least one and preferably two mutations inrelation to the reference sequence SEQ ID No. 8, in a biological sampleaccording to which the biological sample is brought into contact with atleast one ligand specific for said polypeptide, and then the formationof a complex between said polypeptide and said ligand is detected. Thedefinition of ligand corresponds to that defined above. It may be, interalia, a monolonal antibody, a polyclonal antibody, a substrate withenzymatic activity or an enzyme for which said polypeptide is acofactor, or a receptor.

It is also possible to bring the biological sample into contact with aligand specific for the reference polypeptide SEQ ID No. 9 and at leastone ligand specific for at least one other polypeptide as defined above,and then the formation of complexes between said polypeptides and saidligands specific for said polypeptides is detected; it being understoodthat the expression ligand is understood to mean a molecule whichsatisfies the conditions described above.

Another subject of the invention is a nucleotide fragment encoding allor part of the polypeptide SEQ ID No. 9, and its use to obtain adiagnostic, prognostic, prophylactic or therapeutic composition fordetecting, prognosticating, preventing or treating a pathologicalcondition associated with a degenerative and/or autoimmune disease,optionally in combination with at least one nucleotide fragment asdefined above, and the fragments complementary to said fragments.

The expression polypeptide fragment is understood to mean at least allor part of the peptide sequence of a protein, in particular apolypeptide fragment which comprises between about 5 and 15 amino acidsand more precisely between about 5 and 10 amino acids and 6 and 15 aminoacids. The expression nucleotide fragment is understood to mean at leastall or part of a nucleotide sequence, it being understood that theexpression nucleotide sequence covers DNA and RNA sequences.

In particular, the expression polypeptide or nucleotide fragment isunderstood to mean either fragments associated with the same molecularunit, or fragments in a molecular complex comprising several homologousor heterologous subunits obtained naturally or artificially, inparticular by differential multiple splicing or by selective synthesis.

The invention also relates to a method for detecting at least onepolypeptide as defined above, according to which a sample of abiological fluid is collected from a patient having a pathologicalcondition associated with a degenerative and/or neurological and/orautoimmune disease and, optionally after purification of said sample ofbiological fluid, the mass profile obtained from the biological fluid isanalyzed by mass spectrometry and compared with a reference massprofile.

The present invention also relates to the use of at least onepolypeptide of the invention to define therapeutically effective agents,and the use of these agents to prevent and/or treat an autoimmune and/orneurological and/or degenerative disease, and in particular multiplesclerosis.

Thus, other subjects of the invention are the following:

Use of at least one polypeptide comprising at least one fragment of aprotein to test the efficacy of a therapeutic agent, said protein beingchosen from the proteins whose peptide sequence in the native statecorresponds to SEQ ID No. 1, SEQ ID No. 2, SEQ ID No. 3, SEQ ID No. 4,SEQ ID No. 5, SEQ ID No. 6, SEQ ID No. 7, SEQ ID No. 8, SEQ ID No. 9,SEQ ID No. 10, SEQ ID No. 11, SEQ ID No. 12, SEQ ID No. 13, SEQ ID No.14, SEQ ID No. 15, SEQ ID No. 16, SEQ ID No. 17, SEQ ID No. 18, SEQ IDNo. 19, SEQ ID No. 20, SEQ ID No. 21, SEQ ID No. 22, SEQ ID No. 23, SEQID No. 24, SEQ ID No. 25, SEQ ID No. 26, SEQ ID No. 27, SEQ ID No. 28and SEQ ID No. 29, the peptide sequences which exhibit at least 70%identity, preferably at least 80% identity and advantageously at least98 identity with any one of the peptide sequences SEQ ID No. 1 to 29,and the peptide sequences or the fragments of said sequences belongingto the same family of proteins chosen from Perlecan, the precursor ofthe retinol-binding plasma protein, GM2 activator protein, calgranulin Band saposin B;

Use of at least one polypeptide comprising at least one fragment of aprotein to define a biological material for the preparation of apharmaceutical composition for treating a degenerative and/orneurological and/or autoimmune disease, such as multiple sclerosis, saidprotein being chosen from the proteins whose peptide sequence in thenative state corresponds to SEQ ID No. 1, SEQ ID No. 2, SEQ ID No. 3,SEQ ID No. 4, SEQ ID No. 5, SEQ ID No. 6, SEQ ID No. 7, SEQ ID No. 8,SEQ ID No. 9, SEQ ID No. 10, SEQ ID No. 11, SEQ ID No. 12, SEQ ID No.13, SEQ ID No. 14, SEQ ID No. 15, SEQ ID No. 16, SEQ ID No. 17, SEQ IDNo. 18, SEQ ID No. 19, SEQ ID No. 20, SEQ ID No. 21, SEQ ID No. 22, SEQID No. 23, SEQ ID No. 24, SEQ ID No. 25, SEQ ID No. 26, SEQ ID No. 27,SEQ ID No. 28 and SEQ ID No. 29, the peptide sequences which exhibit atleast 70% identity, preferably at least 80% identity and advantageouslyat least 98 identity with any one of the peptide sequences SEQ ID No. 1to 29, and the peptide sequences or the fragments of said sequencesbelonging to the same family of proteins chosen from Perlecan, theprecursor of the retinol-binding plasma protein, GM2 activator protein,calgranulin and saposin;

According to an advantageous variant of one of the preceding uses, thepolypeptide is chosen from SEQ ID No. 2, 4, 8, 9, 17, 24;

Use of at least one nucleotide fragment to test the efficacy of atherapeutic agent for a pathological condition associated with adegenerative and/or neurological and/or autoimmune disease, according towhich said nucleotide fragment is chosen from the fragments which encodeat least one fragment of a protein, said protein being chosen from theproteins whose peptide sequence in the native state corresponds to SEQID No. 1, SEQ ID No. 2, SEQ ID No. 3, SEQ ID No. 4, SEQ ID No. 5, SEQ IDNo. 6, SEQ ID No. 7, SEQ ID No. 8, SEQ ID No. 9, SEQ ID No. 10, SEQ IDNo. 11, SEQ ID No. 12, SEQ ID No. 13, SEQ ID No. 14, SEQ ID No. 15, SEQID No. 16, SEQ ID No. 17, SEQ ID No. 18, SEQ ID No. 19, SEQ ID No. 20,SEQ ID No. 21, SEQ ID No. 22, SEQ ID No. 23, SEQ ID No. 24, SEQ ID No.25, SEQ ID No. 26, SEQ ID No. 27, SEQ ID No. 28 and SEQ ID No. 29, thepeptide sequences which exhibit at least 70% identity, preferably atleast 80% and advantageously at least 98% identity with any one of thepeptide sequences SEQ ID No. 1 to 29, and the fragments complementary tosaid fragments and the fragments which encode the peptide sequences orthe fragments of said sequences belonging to the same family of proteinschosen from Perlecan, the precursor of the retinol-binding plasmaprotein, GM2 activator protein, calgranulin B and saposin B.

Use, to test the efficacy of a therapeutic agent for a pathologicalcondition associated with a degenerative and/or neurological and/orautoimmune disease, of recombinant proteins and/or proteins encoded byall or part of the nucleotide fragments defined in the above paragraph;

Use of at least one nucleotide fragment for the preparation of apharmaceutical composition for treating a degenerative and/orneurological and/or autoimmune disease, such as multiple sclerosis,according to which said nucleotide fragment is chosen from fragmentswhich encode at least one fragment of a protein, said protein beingchosen from the proteins whose peptide sequence in the native statecorresponds to SEQ ID No. 1, SEQ ID No. 2, SEQ ID No. 3, SEQ ID No. 4,SEQ ID No. 5, SEQ ID No. 6, SEQ ID No. 7, SEQ ID No. 8, SEQ ID No. 9,SEQ ID No. 10, SEQ ID No. 11, SEQ ID No. 12, SEQ ID No. 13, SEQ ID No.14, SEQ ID No. 15, SEQ ID No. 16, SEQ ID No. 17, SEQ ID No. 18, SEQ IDNo. 19, SEQ ID No. 20, SEQ ID No. 21, SEQ ID No. 22, SEQ ID No. 23, SEQID No. 24, SEQ ID No. 25, SEQ ID No. 26, SEQ ID No. 27, SEQ ID No. 28and SEQ ID No. 29, the peptide sequences which exhibit at least 70%identity, preferably at least 80% and advantageously at least 98%identity with any one of the peptide sequences SEQ ID No. 1 to 29, andthe fragments complementary to said fragments and the fragments whichencode the peptide sequences or the fragments of said sequencesbelonging to the same family of proteins chosen from Perlecan, theprecursor of the retinol-binding plasma protein, GM2 activator protein,calgranulin B and saposin B;

Use, for the preparation of a pharmaceutical composition for treating adegenerative and/or neurological and/or autoimmune disease, such asmultiple sclerosis, of recombinant proteins and/or proteins encoded byall or part of the nucleotide fragments defined in the precedingparagraph.

Advantageously, said nucleotide fragment used encodes said protein.

Preferably, the peptide sequence of said protein in the native stateconsists of a sequence chosen from any one of SEQ ID No. 1 to 29, thepeptide sequences which exhibit at least 70% identity, preferably atleast 80% identity and advantageously at least 98 identity with any oneof the peptide sequences SEQ ID No. 1 to 29, and the peptide sequencesor the fragments of said sequences belonging to the same family ofproteins chosen from Perlecan, the precursor of the retinol-bindingplasma protein, GM2 activator protein, calgranulin B and saposin B. Thepolypeptides are preferably chosen from SEQ ID No. 2, 4, 8, 9, 17, 24.

Use of at least one nucleotide fragment to test the efficacy of atherapeutic agent for a pathological condition associated with adegenerative and/or neurological and/or autoimmune disease, according towhich said fragment is a fragment of a nucleic sequence chosen from anyone of SEQ ID No. 30, SEQ ID No. 31, SEQ ID No. 32, SEQ ID No. 33, SEQID No. 34, SEQ ID No. 35, SEQ ID No. 36, SEQ ID No. 37, SEQ ID No. 38,SEQ ID No. 39, SEQ ID No. 40, SEQ ID No. 41, SEQ ID No. 42, SEQ ID No.43, SEQ ID No. 44, SEQ ID No. 45, SEQ ID No. 46 and SEQ ID No. 47, SEQID No. 48, SEQ ID No. 49 and SEQ ID No. 50, SEQ ID No. 51, SEQ ID No.52, SEQ ID No. 53, SEQ ID No. 54, SEQ ID No. 55, SEQ ID No. 56, SEQ IDNo. 57, SEQ ID No. 66, SEQ ID No. 67, SEQ ID No. 69, SEQ ID No. 70, SEQID No. 71, and their complementary sequences.

Use of at least one nucleotide fragment for the preparation of apharmaceutical composition for treating a degenerative and/orneurological and/or autoimmune disease, such as multiple sclerosis,according to which said fragment is a fragment of a nucleic sequencechosen from any one of SEQ ID No. 30, SEQ ID No. 31, SEQ ID No. 32, SEQID No. 33, SEQ ID No. 34, SEQ ID No. 35, SEQ ID No. 36, SEQ ID No. 37,SEQ ID No. 38, SEQ ID No. 39, SEQ ID No. 40, SEQ ID No. 41, SEQ ID No.42, SEQ ID No. 43, SEQ ID No. 44, SEQ ID No. 45, SEQ ID No. 46 and SEQID No. 47, SEQ ID No. 48, SEQ ID No. 49 and SEQ ID No. 50, SEQ ID No.51, SEQ ID No. 52, SEQ ID No. 53, SEQ ID No. 54, SEQ ID No. 55, SEQ IDNo. 56, SEQ ID No. 57, SEQ ID No. 66, SEQ ID No. 67, SEQ ID No 68, SEQID No. 69, SEQ ID No. 70, SEQ ID No. 71, and their complementarysequences.

The nucleic sequence is preferably chosen from SEQ ID No. 30, 31, 42,53.

Use of lycorine for the preparation of a composition for preventingand/or treating a degenerative and/or neurological and/or autoimmunedisease.

The expression therapeutic efficacy is understood to mean the clinicaland biological benefit acquired after administration of a therapeuticagent for the purpose of improving or even curing the disease. Thisbenefit is manifested, inter alia, by a reduction in the clinical andbiological signs, and in the pathological effects of the disease afterclinical analysis by the doctor and/or biological analyses, such asmagnetic resonance imaging, analysis of the oligoclonal bands in thecerebrospinal fluid, analysis of evoked potentials and the test fordetection of gliotoxicity called bioassay, whose principle is describedin patent application WO 98/11439 cited above. This reduction in theclinical signs and pathological effects should result in a benefit forthe patient (Schwartz and Lazar, 1995, Elements de statistique médicaleet biologique, eds Flammarion; Lazar and Schwartz, 1995, Eléments destatistique médicale et biologique, eds Flammarion). The disease studiedis preferably multiple sclerosis.

The expression composition for prophylactic and/or therapeutic use isunderstood to mean any composition which comprises an effectivetherapeutic agent. These therapeutic agents are capable (i) ofqualitatively and/or quantitatively influencing the biological activityand/or the function of the proteins of interest identified in thepresent invention, preferably the gliotoxic activity and/or (ii)modulating and/or inhibiting the expression of these proteins and/or(iii) reducing the concentration of these proteins in an extracellularand/or intracellular compartment, and/or substituting a nonpathogenicform for a pathogenic, for example mutated, form of one of theseproteins and/or modulating their attachment to at least one of theirligands; said ligand being a molecule which satisfies the criteriadescribed above. Various therapeutic agents are produced based on theconventional approaches widely described in the literature. The variousgroups of therapeutic agents defined from the proteins of interestidentified in this present invention are described below. Theirprophylactic and/or therapeutic efficacy or activity is evaluated invitro and/or in vivo.

Evaluation of the efficacy of a therapeutic agent in vitro: urinesamples from healthy individuals and from patients suffering frommultiple sclerosis, preferably in the active phase, are tested for theirgliotoxic activity in vitro based on the bioassay protocol described inpatent application WO 98/11439, cited above. The experiment is carriedout in parallel by adding or otherwise, to the urine samples tested, thetherapeutic agent whose efficacy is to be tested. Assays are carried outat various concentrations of this agent, and after various incubationtimes with the sample, at a temperature of about 37° C. or at roomtemperature, for each concentration of agent tested, before carrying outthe bioassay test. The gliotoxic activity is determined for each crudeor purified sample of control and patient's urine in the presence or inthe absence of tested therapeutic agent. A prophylactic and/ortherapeutic agent for multiple sclerosis is an agent which allows areduction or an inhibition of the gliotoxic activity in a biologicalfluid from the patients, in particular in the urine. This reduction orinhibition is evaluated relative to the gliotoxic activity detected inthe biological fluid of MS patients in the absence of the test agentwhich defines the upper limit and relative to the gliotoxic activitydetected in the urine of a healthy individual which determines the lowerlimit (Schwartz and Lazar, 1995, Elements de statistique médicale etbiologique, eds Flammarion; Lazar and Schwartz, 1995, Elements destatistique médicale et biologique, eds Flammarion). The therapeuticefficacy of several agents may be evaluated in combination in the sameassay.

Evaluation of the efficacy of a therapeutic agent using an animal model:there are injected into an animal fractions of purified urine and/or atleast one polypeptide of the invention and/or at least one proteinobtained by genetic recombination which corresponds to at least onepolypeptide of the invention and/or at least one synthetic polypeptidewhose amino acid sequence corresponds to the sequence of at least onepolypeptide of the invention. The injections are carried out, at variousestablished concentrations, into mammalian animals such as mice or rats,preferably a Lewis rat according to the protocol described in patentapplication WO97/33466 cited above. Various concentrations of a fractionof crude or purified urine or of at least one polypeptide and/or oneprotein, as defined above, are injected into a series of animals by theintradermal, intravenous, intrathecal, intracerebral or intramuscularroute, and the like. A negative control is carried out in parallel. Theprophylactic and/or therapeutic agent to be evaluated and then injectedat various concentrations and by various routes of administration to amammalian animal, preferably to a mouse or to a rat. The injections arecarried out as a single dose or as repeated doses, with various timeintervals between each administration. A few hours to a few weeks afterthe administration, biological samples, preferably of blood, serum,cerebrospinal fluid, or urine, are collected. These samples aresubjected to:

(i) a measurement of the gliotoxic activity by the bioassay, and/or

(ii) a measurement of activity of the polypeptides and/or proteins ofinterest of the invention, alone or in combination, as described atleast in: Li et al., 1983, Am J Hum Genet 35:629–634; Li et al., 1988 JBiol Chem 263:6588–6591; Li et al., 1981 J Biol Chem 256: 6234–6240; Liet al., 1976 J Biol Chem 251:1159; Kase et al., 1996, FebsLetters 393:74–76; Kishimoto et al., 1992, J Lipid Res 33: 1255–1267; O'Brien etal., 1991 Faseb J 5: 301–308; Murthy et al., 1993 J Immunol 151:6291–6301; Murao et al., 1990 Cell growth Differ 1: 447–454, and/or(iii) an assay of the polypeptides and/or proteins of interest, alone orin combination, by ELISA (Enzyme Linked-Immunosorbant Assay) and/orWestern blotting, using antibodies or antibody fragments capable ofbinding to at least one of the polypeptides and/or proteins of theinvention, or their fragment, and/or(iv) an assay of antibodies specific for the polypeptides and/orproteins of interest or their fragments, alone or in combination or theassay of at least one ligand capable of binding to the polypeptidesand/or proteins of interest or their fragments, and/or(v) an assay of the “helper” and/or cytotoxic cellular immune responseinduced against the polypeptides and proteins of interest or theirfragments and any immunogenic peptide derived from these polypeptides,proteins and fragments, by carrying out, for example, a test ofactivation in vitro of “helper” T lymphocyte cells specific for theantigen administered; by quantifying the cytotoxic T lymphocytesaccording to the so-called ELISPOT technique described by Scheibenbogenet al., 1997 Clinical Cancer Research 3: 221–226. Such a determinationis particularly advantageous when it is desired to evaluate the efficacyof a vaccine approach for use in a given patient or for diagnosingand/or prognosticating a potential pathological condition by seeking todemonstrate an immune response naturally developed by the patientagainst the antigen, the polypeptides, the proteins of interest or theimmunogenic fragments derived from these proteins.

The expression “ligand capable of binding to a protein” is understood tomean any molecule capable of recognizing the protein or a portion of theprotein. This may be verified for example in vitro by Elisa and/orWestern blot tests.

The expression “polypeptides and/or proteins of interest of theinvention” designates the C-terminal fragment of Perlecan (SEQ ID No.2), the precursor of the retinol-binding plasma protein (SEQ ID No. 4),the GM2 activator protein (SEQ ID No. 8), the mutated protein of the GM2activator (SEQ ID No. 9), calgranulin B (SEQ ID No. 17), saposin B (SEQID No. 24), the proteins or fragments belonging to the family of theprecursor of the retinol-binding plasma protein (for example SEQ ID No.5 to 7), the proteins or fragments belonging to the family of the GM2activator protein (for example SEQ ID No. 10 to 16), the proteins orfragments belonging to the family of calgranulin B protein (for exampleSEQ ID No. 18 to 23), the proteins or fragments belonging to the familyof the saposin B protein (for example SEQ ID No. 25 to 29) and thepeptide sequences which exhibit at least 70% identity, preferably atleast 80% identity and advantageously at least 98% identity with any oneof the peptide sequences SEQ ID No. 1 to 29.

The animal is then sacrificed and histological sections of varioustissues are prepared, preferably brain sections. Various studies andobservations are carried out in order to detect and/or quantify thecharacteristic effects of the polypeptides and/or active proteinsassociated with the gliotoxic fraction, that is to say an apoptosis ofthe glial cells, and/or the opening of the blood-brain barrier and/or ademyelination. The presence or the expression of the polypeptides and/orproteins of interest identified is also observed and/or quantified inthese tissues:

(i) by conventional immunohistological analyses using ligands for thepolypeptides and/or proteins of interest and/or their fragments and/ormonoclonal or polyclonal antibodies or fragments of said which bind tothe polypeptides and/or proteins of interest, or to their fragments,and/or(ii) by conventional in situ hybridization techniques using nucleic acidfragments or oligonucleotides defined from polypeptide and/or proteinsequences of interest; and/or(iii) by PCR and/or RT-PCR amplification techniques in situ usingnucleic acid fragments or primers defined from polypeptide and/orprotein sequences of interest.

The expression antibodies capable of binding to a polypeptide, to aprotein or to their fragments is understood to mean any monoclonal orpolyclonal antibody and any fragment of said antibodies capable ofrecognizing the polypeptide, the protein or their fragments. Thecapacity of the antibodies to recognize said polypeptides, proteins ortheir fragments is verified in vitro, for example by ELISA and/orWestern blotting. An antibody capable of binding to the saposin Bprotein (SEQ ID No. 24) or to any fragment of this protein is describedby Misasi et al. 1998, J. NeuroChem. 71:2313 and Klein et al. 1994, BBRC200: 1440–1448 or may be produced using conventional methods, forexample those designated by references above for the production ofmonoclonal and polyclonal antibodies, by immunization starting with anatural protein, a recombinant protein, a synthetic polypeptide or theirfragments. The immunogenic peptides for the production of anti-saposin Bmonoclonal antibodies are the peptides corresponding to the sequencesSEQ ID No. 61 and SEQ ID No. 62.

For example, an antibody capable of binding to the GM2 activator protein(SEQ ID No. 8) or to any fragment of this protein is illustrated byYuziuk et al., 1998 J Biol Chem 273: 66–72 or may be produced usingconventional methods known to persons skilled in the art. This antibodymay for example be produced after injecting into mice or rabbits thenatural protein or any fragment, and/or the recombinant protein or anyfragment, and/or peptides defined and synthesized from the proteinsequence of the protein. The immunogenic peptides used for theproduction of anti-GM2 monoclonal antibodies are the reference peptidesSEQ ID No. 58, SEQ ID No. 59 and SEQ ID No. 60. An antibody capable ofbinding to the galgranulin B protein (SEQ ID No. 17) or to any fragmentof this protein is described by Saintigny et al., 1992 J Invest Dermatol99: 639–644 and Goebeler et al. 1994 J Leukoc Biol 55: 259–261, or maybe produced using conventional methods. The immunogenic peptides for theproduction of anti-calgranulin B monoclonal antibodies are the peptidescorresponding to the sequences SEQ ID No. 63, SEQ ID No. 64 and SEQ IDNo. 65. An antibody capable of binding to the mutated GM2 activatorprotein (SEQ ID No. 9) or to any fragment of this protein may beproduced using the conventional methods defined above.

The expression natural protein and fragment is understood to mean anyisolated, completely or partially purified protein obtained from a humanor animal sample and any fragment obtained from this protein. Forexample, the natural protein corresponding to saposin B (SEQ ID No. 24)is obtained according to the technique described by Waring et al. 1998Mol Genet Metab 63: 14–25; the natural protein corresponding to the GM2activator protein (SEQ ID No. 8) according to the technique described byDeGasperi et al., 1989 Biochem J 260: 777–783, Vogel et al., 1987 ArchBiochem Biophys 259: 627–638, Mitsuyama, 1983 Hokkaido Igaku Zasshi 58:502–512; Hirabayashi et al 1983 J Neurochem 40: 168–175, Conzelmann etal., 1979 Hoppe Seylers Z Physiol Chem 360: 1837–1849, Li et al., 1976 JBiol Chem 251: 1159–1163. The natural protein corresponding tocalgranulin B (SEQ ID No. 17) is obtained according to the techniquedescribed by Hitomi et al., 1996 J Cell Sci 109: 805–815, Van den Bos etal. 1998 Protein Expr Purif 13: 313–318 and Raftery et al. 1996 BiochemJ 316: 285–293.

The expression recombinant protein or fragment of a recombinant proteinrefers to any protein or protein fragment produced in a prokaryotic oreukaryotic cell from a nucleotide sequence encoding the protein or itsfragment and transfected into the cell, this protein or its fragmentthen being purified. In general, any cell derived from a prokaryotic oreukaryotic organism may be used in the context of the present invention,but the cells derived from eukaryotic organisms are preferred. There maybe mentioned, by way of example, CHO cells, COS cells, and Semlikicells. For the purposes of the present invention, said cell may be wildtype or mutant. For example, the recombinant protein corresponding tosaposin B (SEQ ID No. 24) may be obtained according to the techniquesdescribed by Zaltash et al. 1998 Bebbs letter 423: 1–4 and Qi et al.1994 J Biol Chem 269: 16746–16753. Such a recombinant protein is atleast available from Kase et al. 1996 Febs Lett 393: 74–76. Therecombinant protein corresponding to the GM2 activator protein (SEQ IDNo. 8) may be produced by the techniques described by Yuziuk et al. 1998J Biol Chem 273: 66–72 and Bierfreund et al., 1999 Neurochem Res 24:295–300. The recombinant protein corresponding to calgranulin B (SEQ IDNo. 17) may be obtained according to the protocol by Longbottom et al.1992 Biochim Biophys Acta 1120:215–222, Raftery et al. 1999 Protein ExprPurif 15:228–235. Such a recombinant protein is available at least fromKlempt et al. 1997 Febs Letter 408:81–84.

The expression DNA nucleotide sequence or DNA nucleotide fragmentencoding all or part of the saposin B protein (SEQ ID No. 24) isunderstood to mean the nucleic acid sequence SEQ ID No. 53 or a fragmentof this sequence. The expression RNA nucleotide sequence or fragmentencoding all or part of the saposin B protein (SEQ ID No. 24) isunderstood to mean any sequence deduced from the DNA sequence SEQ ID No.53, taking into account the genetic code and the splicing phenomena.

The expression DNA nucleotide sequence or DNA nucleotide fragmentencoding all or part of the GM2 activator protein (SEQ ID No. 8) isunderstood to mean the nucleic acid sequence SEQ ID No. 31 or a fragmentof this sequence. The expression RNA nucleotide sequence or fragmentencoding all or part of the GM2 activator protein (SEQ ID No. 8) isunderstood to mean any sequence deduced from the DNA sequence SEQ ID No.31, taking into account the genetic code and the splicing phenomena.

The expression DNA nucleotide sequence or DNA nucleotide fragmentencoding all or part of the calgranulin B protein (SEQ ID No. 17) isunderstood to mean the nucleic acid sequence SEQ ID No. 42 or a fragmentof this sequence. The expression RNA nucleotide sequence or fragmentencoding all or part of the calgranulin B protein (SEQ ID No. 17) isunderstood to mean any sequence deduced from the DNA sequence SEQ ID No.42, taking into account the genetic code and the splicing phenomena.

The expression nucleotide sequence or fragment encoding all or part ofthe mutated protein (SEQ ID No. 9) is understood to mean the nucleicacid sequence deduced from the sequence SEQ ID No. 9, taking intoaccount the genetic code. The expression RNA nucleotide sequence orfragment encoding all or part of this mutated B protein (SEQ ID No. 9)is understood to mean any sequence deduced from the DNA sequence, takinginto account the genetic code and the splicing phenomena.

The expression protein activity is understood to mean a characteristicbiological function of the protein. The protein activity may bedemonstrated by techniques known to persons skilled in the art. Forexample, the activity of saposin B (SEQ ID No. 24) and of the proteinsof the saposin B family (for example SEQ ID No. 25 to 29) may bedetected using the protocols described by Li et al., 1983, Am J HumGenet 35:629–634; Li et al., 1988 J Biol Chem 263: 6588–6591, Li et al.,1981 J Biol Chem 256: 6234–6240 and Li et al., 1976 J Biol Chem251:1159. The expression activity of the GM2 activator protein (SEQ IDNo. 8) and of the proteins of the same family (for example SEQ ID No. 10to 16) is understood to mean at least the activity detected using theprotocols described, for example, by Kase et al., 1996, Febs Letters393: 74–76, Kishimoto et al., 1992, J Lipid Res 33:1255–1267 and O'Brienet al., 1991 Faseb J 5: 301–308. The expression activity of calgranulinB (SEQ ID No. 17) and the proteins of the same calgranulin B family (forexample SEQ ID No. 18 to 23) and any is understood to mean at least theactivity detected using the protocols described for example by Murthy etal., 1993 J Immunol 151: 6291–6301 and Murao et al., 1990 Cell growthDiffer 1: 447–454.

Production of a transgenic animal, preferably murine, model for a humanpathology can be technically achieved. Briefly, the transgenic animal isproduced using the conventional techniques described and possesses,integrated into the genome, the nucleic acids encoding the proteins ortheir fragments.

Evaluation of the efficacy of a therapeutic agent and therapeuticmonitoring ex vivo, in humans:

the therapeutic agents to be tested for a therapeutic activity and/orfor therapeutic monitoring are administered by various routes to humans,such as the intradermal, intravenous, intramuscular, intracerebral ororal routes, and the like. Various doses are administered to humanbeings. The patient's clinical file at the time of the firstadministration is perfectly known. One or more administrations may becarried out with various time intervals between each administrationwhich may range from a few days to a few years. Biological samples arecollected at defined time intervals after administration of thetherapeutic agent, preferably blood, serum, cerebrospinal fluid andurine. Various analyses are carried out using these samples. Immediatelybefore the first administration of the therapeutic agent, these samplecollections and these same analyses are again performed. A conventionalclinical and biological examination (MRI, oligoclonal bands incerebrospinal fluid, evoked potentials) is also carried out in parallelwith the additional analyses which are described below, at variousanalytical times. The analyses carried out are:(i) a measurement of the gliotoxic activity by bioassay starting withsamples of serum, CSF and urine, and/or(ii) a measurement of the activity of proteins of interest identified inthe present invention alone or in combination, as described for exampleby: Li et al., 1983, Am J Hum Genet 35:629–634; Li et al., 1988 J BiolChem 263: 6588–6591; Li et al., 1981 J Biol Chem 256: 6234–6240; Li etal., 1976 J Biol Chem 251:1159; Kase et al., 1996, FebsLetters393:74–76; Kishimoto et al., 1992, J Lipid Res 33: 1255–1267; O'Brien etal., 1991 Faseb J 5: 301–308; Murthy et al., 1993 J Immunol 151:6291–6301; Murao et al., 1990 Cell growth Differ 1: 447–454; and/or(iii) an assay of the proteins of interest or of their fragments, aloneor in combination, in the blood/serum, CSF or urine samples by ELISAand/or Western blotting, using antibodies or antibody fragments capableof binding to at least one of the proteins or to one of their fragments,and/or(iv) an assay of antibodies specific for the proteins of interest or oftheir fragments in blood/serum, CSF or urine samples, by ELISA and/orWestern blotting using a natural protein or a fragment of the naturalprotein and/or a recombinant protein or a fragment of this recombinantprotein, alone or in combination. Likewise, an assay of ligands capableof binding to the proteins of interest identified, alone or incombination, may be carried out, and/or(v) an assay of “helper” and/or cytotoxic cellular immune responseinduced against the proteins of interest and any immunogenic peptidederived from these proteins, for example by carrying out a test ofactivation in vitro of T lymphocyte cells specific for the antigenadministered (example). For example, using a test of activation in vitroof helper T lymphocyte cells specific for the antigen administered(example); For example by quantifying the cytotoxic T lymphocytesaccording to the so-called ELISPOT technique described by Scheibenbogenet al., 1997 Clinical Cancer Research 3: 221–226. Such a determinationis particularly advantageous when it is desired to evaluate the efficacyof a vaccine approach used in a given patient or to diagnose a potentialpathological condition in a patient, seeking to demonstrate an immuneresponse naturally developed by said patient against the antigen, theproteins of interest or any immunogenic fragment derived from theseproteins, alone or in combination, and/or(vi) a detection of DNA and/or RNA fragments encoding the proteins or afragment of proteins of interest by nucleotide hybridization accordingto techniques well known to persons skilled in the art (Southernblotting, Northern blotting, ELOSA “Enzyme-linked Oligosorbent Assay”(Katz J B et al., Am. J. Vet. Res., 1993 December; 54 (12):2021–6 andFrancois Mallet et al., Journal of Clinical Microbiology, June 1993, p1444–1449)) and/or by the DNA and/or RNA amplification method, forexample by PCR, RT-PCR, using nucleic acid fragments encoding thesequence of the proteins of interest, and/or(vii) by tissue, preferably brain, biopsy and observation of thecharacteristic effects of the active proteins associated with thegliotoxic fraction, that is to say an apoptosis of the glial cellsand/or the opening of the blood-brain barrier and/or the observation ofdemyelination phenomena, and/or(viii) by tissue biopsy or on circulating cells (blood, CSF),observation of the presence of proteins of interest and estimation oftheir expression by immunohistological observation on histologicalsections prepared from tissues, using ligands and/or antibodies or theirfragments capable of binding to the proteins of interest, and/or(ix) by tissue biopsy or on circulating cells (blood, CSF), observationof the expression of the proteins of interest by in situ hybridizationof the RNA molecules encoding the proteins of interest using nucleicacids defined using the sequences of the proteins of interest, and/or(x) by tissue biopsy or on circulating cells (blood, CSF), determinationof the expression of the proteins of interest by amplification of theseRNAs by conventional techniques such as, for example, RT-PCR, usingnucleic acids defined using the sequences of the proteins of interest.

The expression “polypeptides and/or proteins of interest of theinvention” designates the C-terminal fragment of Perlecan (SEQ ID No.2), the precursor of the retinol-binding plasma protein (SEQ ID No. 4),the GM2 activator protein (SEQ ID No. 8), the mutated GM2 activatorprotein (SEQ ID No. 9), calgranulin B (SEQ ID No. 17), saposin B (SEQ IDNo. 24), the proteins or fragments belonging to the family of theprecursor of the retinol-binding plasma protein (for example SEQ ID No.5 to 7), the proteins or fragments belonging to the family of the GM2activator protein (for example SEQ ID No. 10 to 16), the proteins orfragments belonging to the calgranulin B protein family (for example SEQID No. 18 to 23), the proteins or fragments belonging to the saposin Bprotein family (for example SEQ ID No. 25 to 29), and the peptidesequences which exhibit at least 70% identity, preferably at least 80%identity and advantageously at least 98 identity with any one of thepeptide sequences SEQ ID No. 1 to 29.

The expression DNA nucleic acid sequence or fragments encoding the“polypeptides and/or proteins of interest of the invention” designatesthe nucleic acid sequence encoding the C-terminal fragment of Perlecan(SEQ ID No. 2), the nucleic acid sequence encoding the precursor of theretinol-binding plasma protein (SEQ ID No. 4), the nucleic acid sequence(SEQ ID No. 31) encoding the GM2 activator protein (SEQ ID No. 8), thenucleic acid sequence encoding the mutated GM2 activator protein (SEQ IDNo. 9), the nucleic acid sequence (SEQ ID No. 42) encoding calgranulin B(SEQ ID No. 17), the nucleic acid sequence (SEQ ID No. 53) encodingsaposin B (SEQ ID No. 24), the DNA and RNA nucleic acid sequences (SEQID No. 30 to 57) encoding the proteins or fragments belonging to thefamily of the precursor of the retinol-binding plasma protein (forexample SEQ ID No. 5 to 7), the proteins or fragments belonging to thefamily of the GM2 activator protein (for example SEQ ID No. 10 to 16),the proteins or fragments belonging to the calgranulin B protein family(for example SEQ ID No. 18 to 23), the proteins or fragments belongingto the saposin B protein family (for example SEQ ID No. 25 to 29).

A protein or a variant of a protein chosen more particularly from thesequences defined in the identifiers SEQ ID Nos. 2, 4, 8, 9, 17 and 24or their fragments, or from the sequences corresponding to the proteinsof the families of said sequences (SEQ ID No. 1, SEQ ID No. 3, SEQ IDNo. 5 to 7, SEQ ID No. 10 to 16, SEQ ID No. 18 to 24, SEQ ID No. 25 to29), and the peptide sequences which exhibit at least 70% identity,preferably at least 80% identity and advantageously at least 98 identitywith any one of the peptide sequences SEQ ID No. 1 to 29, independentlyor in combination, exhibits a toxic effect directly or indirectly oncells, in particular on glial cells, which is demonstrated by theabovementioned bioassay. The autoantibodies produced in response to thepresence of this protein or of these proteins are associated with theautoimmune process. Thus, the target of the therapeutic agent(s) is forexample (i) the natural protein or the natural proteins or theirvariants with the aim of regulating their expression and/or theirintracellular concentration and/or their concentration in thebloodstream, (ii) an antibody specific for at least such a protein. Thetherapeutic agent or the therapeutic agents defined eliminate the targetdirectly, by inducing a specific immune response, and/or neutralize it.

The present invention therefore relates to a biological material for thepreparation of a pharmaceutical composition for treating mammalssuffering from degenerative and/or autoimmune and/or neurologicalpathological conditions, preferably multiple sclerosis, said compositioncomprising:

(i) either at least one natural protein and/or one recombinant proteinor their fragments whose sequence corresponds to all or part of thesequences designated by the references SEQ ID No. 2, 4, 8, 9, 17 and 24and the peptide sequences or the fragments of said sequences belongingto the same family of proteins chosen from Perlecan, the precursor ofthe retinol-binding plasma protein, GM2 activator protein, calgranulin Band saposin B (for example SEQ ID No. 1, SEQ ID No. 3, SEQ ID No. 5 to7, SEQ ID No. 10 to 16, SEQ ID No. 18 to 23, SEQ ID No. 25 to 29), andthe peptide sequences which exhibit at least 70% identity, preferably atleast 80% identity and advantageously at least 98 identity with any oneof the peptide sequences SEQ ID No. 1 to 29, independently or incombination,(ii) or at least one ligand specific for at least one of said proteinsor their fragments whose sequence corresponds to all or part of thesequences designated by the references SEQ ID No. 2, 4, 8, 9, 17 and 24,and the peptide sequences or the fragments of said sequences belongingto the same family of proteins chosen from Perlecan, the precursor ofthe retinol-binding plasma protein, GM2 activator protein, calgranulin Band saposin B (for example SEQ ID No. 1, SEQ ID No. 3, SEQ ID No. 5 to7, SEQ ID No. 10 to 16, SEQ ID No. 18 to 23, SEQ ID No. 25 to 29), andthe peptide sequences which exhibit at least 70% identity, preferably atleast 80% identity and advantageously at least 98 identity with any oneof the peptide sequences SEQ ID No. 1 to 29, independently or incombination,(iii) or at least one polyclonal or monoclonal antibody specific for atleast one of said proteins or their fragments whose sequence correspondsto all or part of the sequences designated by the references SEQ ID No.2, 4, 8, 9, 17 and 24, and the peptide sequences or the fragments ofsaid sequences belonging to the same family of proteins chosen fromPerlecan, the precursor of the retinol-binding plasma protein, GM2activator protein, calgranulin B and saposin B (for example SEQ ID No.1, SEQ ID No. 3, SEQ ID No. 5 to 7, SEQ ID No. 10 to 16, SEQ ID No. 18to 23, SEQ ID No. 25 to 29), and the peptide sequences which exhibit atleast 70% identity, preferably at least 80% identity and advantageouslyat least 98 identity with any one of the peptide sequences SEQ ID No. 1to 29, independently or in combination,(iv) or at least one nucleic acid sequence comprising at least one geneof therapeutic interest whose nucleic sequence is deduced from the DNAand RNA sequences encoding all or part of the proteins whose sequencesare designated by the references SEQ ID No. 2, 4, 8, 9, 17 and 24, andthe DNA and/or RNA sequences (for example SEQ ID No. 30 to 57) encodingall or part of the proteins belonging to the same family of proteinschosen from Perlecan, the precursor of the retinol-binding plasmaprotein, GM2 activator protein, calgranulin B and saposin B, inassociation with elements ensuring the expression of said gene oftherapeutic interest in vivo in target cells intended to be geneticallymodified by the nucleic sequence of the gene of therapeutic interest,(v) or at least one mammalian cell not naturally producing the proteinof interest or the proteins of interest or any fragment of this or theseprotein(s) or of the antibodies specific for at least one of saidproteins or of its fragments, said mammalian cell being geneticallymodified in vitro by at least one nucleic acid sequence or a fragment ofa nucleic acid sequence or a combination of nucleic acid sequencescorresponding to nucleic acid fragments derived from the same gene orfrom different genes, said nucleic sequence(s) being deduced from theDNA and RNA sequences encoding the proteins designated by the referencesSEQ ID No. 2, 4, 8, 9, 17 and 24, and the DNA and/or RNA sequences (forexample SEQ ID No. 30 to 57) encoding all or part of the proteinsbelonging to the same family of proteins chosen from Perlecan, theprecursor of the retinol-binding plasma protein, GM2 activator protein,calgranulin B and saposin B, said gene of therapeutic interest encodingall or part of the protein of interest, of a fragment of the protein ofinterest or of an antibody specific for the protein of interest whichwill be expressed at the surface of said mammalian cell (Toes et al.,1997, PNAS 94: 14660–14665). The pharmaceutical composition may containa therapeutic agent alone directed against a target alone or agentstaken in combination directed against several targets.

The expression “polypeptides and/or proteins of interest of theinvention” designates the C-terminal fragment of Perlecan (SEQ ID No.2), the precursor of the retinol-binding plasma protein (SEQ ID No. 4),the GM2 activator protein (SEQ ID No. 8), the mutated GM2 activatorprotein (SEQ ID No. 9), calgranulin B (SEQ ID No. 17), saposin B (SEQ IDNo. 24), the proteins or fragments belonging to the family of theprecursor of the retinol-binding plasma protein (for example SEQ ID No.5 to 7), the proteins or fragments belonging to the family of the GM2activator protein (for example SEQ ID No. 10 to 16), the proteins orfragments belonging to the calgranulin B protein family (for example SEQID No. 18 to 23), the proteins or fragments belonging to the saposin Bprotein family (for example SEQ ID No. 25 to 29 and the peptidesequences which exhibit at least 70% identity, preferably at least 80%identity and advantageously at least 98% identity with any one of thepeptide sequences SEQ ID No. 1 to 29.

From the knowledge of the amino acid sequences of the proteins ofinterest identified in the present invention, it is within thecapability of persons skilled in the art to define and use the moleculesdescribed above and/or any molecule capable of binding to saidmolecules, and/or any molecule capable of inhibiting said molecules.Thus, the present invention relates to the use of natural and/orrecombinant proteins and/or of synthetic polypeptides and theirfragments, of ligands capable of binding to said proteins or to theirfragment(s), for example antibodies; proteins inhibiting the functionand/or expression and/or binding of said proteins.

Use of natural protein(s) and/or peptide(s) and/or recombinantprotein(s) and/or synthetic polypeptide(s) corresponding to the proteinsof interest identified in the present invention.

The present invention relates to a biological material for thepreparation of pharmaceutical compositions for treating mammalssuffering from an autoimmune disease, preferably multiple sclerosis,comprising:

(i) either at least one natural protein and/or one recombinant proteinand/or one synthetic polypeptide chosen from the proteins whose aminoacid sequences are designated by the references SEQ ID No. 2, 4, 8, 9,17 and 24, and the peptide sequences or the fragments of said sequencesbelonging to the same family of proteins chosen from Perlecan, theprecursor of the retinol-binding plasma protein, GM2 activator protein,calgranulin B and saposin B (for example SEQ ID No. 1, SEQ ID No. 3, SEQID No. 5 to 7, SEQ ID No. 10 to 16, SEQ ID No. 18 to 23, SEQ ID No. 25to 29), and the peptide sequences which exhibit at least 70% identity,preferably at least 80% identity and advantageously at least 98 identitywith any one of the peptide sequences SEQ ID No. 1 to 29, alone or incombination,(ii) or at least one natural and/or synthetic fragment of these proteinsof interest, for example an immunogenic fragment capable of inducing animmune response against a target polypeptide,(iii) or at least one mimotope peptide defined from the referencesequences SEQ ID No. 2, 4, 8, 9, 17 and 24, and the peptide sequences orthe fragments of said sequences belonging to the same family of proteinschosen from Perlecan, the precursor of the retinol-binding plasmaprotein, GM2 activator protein, calgranulin B and saposin B (for exampleSEQ ID No. 1, SEQ ID No. 3, SEQ ID No. 5 to 7, SEQ ID No. 10 to 16, SEQID No. 18 to 23, SEQ ID No. 25 to 29), and the peptide sequences whichexhibit at least 70% identity, preferably at least 80% identity andadvantageously at least 98 identity with any one of the peptidesequences SEQ ID No. 1 to 29, or a combination of mimotopes, capable ofinducing an immune response against the target polypeptide,(iv) or at least any protein or peptide capable of regulating in vivothe transcription and/or the translation of the proteins of interest(SEQ ID No. 2, 4, 8, 9, 17 and 24) and the peptide sequences or thefragments of said sequences belonging to the same family of proteinschosen from Perlecan, the precursor of the retinol-binding plasmaprotein, GM2 activator protein, calgranulin B and saposin B (for exampleSEQ ID No. 1, SEQ ID No. 3, SEQ ID No. 5 to 7, SEQ ID No. 10 to 16, SEQID No. 18 to 23, SEQ ID No. 25 to 29) and the peptide sequences whichexhibit at least 70% identity, preferably at least 80% identity andadvantageously at least 98 identity with any one of the peptidesequences SEQ ID No. 1 to 29. The administration of these proteinsand/or peptides alone or in combination can reestablish theconcentration of a protein of interest in the body.

The immune response directed against a specific antigen may be dividedinto two distinct categories, one involving the antibodies (humoral typeimmune response), the other the cytotoxic effector cells such as forexample the macrophages, the cytotoxic lymphocytes (CTL) or the killer(NK) cells as well as the “helper” T lymphocytes, in particular the CD4+T lymphocytes (cellular type immune response). More particularly, thetwo types of response are distinguishable in that the antibodiesrecognize the antigens under their three-dimensional form whereas the Tlymphocytes, for example, recognize peptide portions of said antigens,associated with glycoproteins encoded by the genes of the majorhistocompatibility complex (MHC), in particular the genes of the type Imajor histocompatibility complex which are ubiquitously expressed at thesurface of the cells or the genes of the type II majorhistocompatibility complex which are specifically expressed at thesurface of the cells involved in the presentation of antigens (APC). 1)According to a first aspect, the cellular type immune response ischaracterized in that the CD4+ type T cells (helper T cells), followinga well-known activation phenomenon (for a review see Alberolalia 1997,Annu Rev Immunol 15, 125–154), produce cytokines which in turn inducethe proliferation of APC cells capable of producing said cytokines, thecellular differentiation of the B lymphocytes capable of producingantibodies specific for the antigen, and the stimulation of thecytotoxic T lymphocytes (CTL). 2) According to a second aspect of thecellular immune response, the cytotoxic effector cells such as forexample the CD8+ type lymphocytes (CTL) are activated a) afterinteraction with antigenic peptides bound to and presented by theglycoproteins carried by the ubiquitous cells and encoded by the genesbelonging to the MHCI system, and b) optionally by the cytokinesproduced by the CD4+ cells.

The present invention relates to the administration of a protein or of apeptide derived from the proteins of interest (SEQ ID No. 2, 4, 8, 9, 17and 24) or of their fragment(s), and the peptide sequences or thefragments of said sequences belonging to the same family of proteinschosen from Perlecan, the precursor of the retinol-binding plasmaprotein, GM2 activator protein, calgranulin B and saposin B (for exampleSEQ ID No. 1, SEQ ID No. 3, SEQ ID No. 5 to 7, SEQ ID No. 10 to 16, SEQID No. 18 to 23, SEQ ID No. 25 to 29), and the peptide sequences whichexhibit at least 70% identity, preferably at least 80% identity andadvantageously at least 98% identity with any one of the peptidesequences SEQ ID No. 1 to 29, alone or in combination, for theprophylaxy and/or the therapy of an autoimmune disease, such as multiplesclerosis. These administered proteins and peptides are characterized inthat they must have lost their toxic activity, for example theirgliotoxic activity, or must have lost their capacity to bind to aligand, and may significantly induce an immune response mediated by theT lymphocytes and/or the antibodies directed against this protein areused. Such proteins are said to be “modified”; nevertheless, theirimmunogenicity is preserved. Such modified immunogenic molecules areobtained by a number of conventional treatments, for example chemical orheat denaturation, truncation or mutation with deletion, insertion orlocation of amino acids. An example of truncation consists in thetruncation of amino acids at the carboxy-terminal end which may be up to5–30 amino acids. The modified molecules may be obtained by syntheticand/or recombinant techniques or by chemical or physical treatments ofthe natural molecules.

The natural and/or recombinant proteins of interest identified in thepresent invention (SEQ ID No. 2, 4, 8, 9, 17 and 25), and the peptidesequences or the fragments of said sequences belonging to the samefamily of proteins chosen from Perlecan, the precursor of theretinol-binding plasma protein, GM2 activator protein, calgranulin B andsaposin B (for example SEQ ID No. 1, SEQ ID No. 3, SEQ ID No. 5 to 7,SEQ ID No. 10 to 16, SEQ ID No. 18 to 23, SEQ ID No. 25 to 29), and thepeptide sequences which exhibit at least 70% identity, preferably atleast 80% identity and advantageously at least 98 identity with any oneof the peptide sequences SEQ ID No. 1 to 29, or their fragment(s), areused in prophylactic and therapeutic vaccination against autoimmunediseases, preferably MS. A vaccine comprises an immunogenicallyeffective quantity of the immunogenic protein in association with apharmaceutically acceptable vehicle and optionally an adjuvant and/or adiluent. The pharmaceutically acceptable vehicles, adjuvants anddiluents are well known to persons skilled in the art. There may bementioned, by way of references, Remington's Pharmaceutical Sciences.The use of vaccine compositions is particularly advantageous inassociation with an early diagnosis of the disease. The immunogenicprotein is used in the preparation of a medicament for prophylactic ortherapeutic vaccination. The proteins of interest may be eliminated fromthe body without inducing undesirable side effects. The identificationof such vaccine proteins or peptides is carried out as follows: thecandidate molecules modified as described above (proteins which arenatural or recombinant, peptides) are analyzed in a functional test toverify that they have lost their toxicity, for example their gliotoxicactivity, using the test known as bioassay, and to verify theirimmunogenicity (i) by carrying out an in vitro test of proliferation ofCD4+ T lymphocytes specific for the antigen administered (T cell assay)or an in vitro test of cytotoxicity of the CD8+ lymphocytes specific forthe antigen administered and (ii) by measuring, inter alia, the amountof circulating antibodies directed against the natural protein. Thesemodified forms are used to immunize humans by standard procedures withappropriate adjuvants.

The prepared vaccines are injectable, that is to say in liquid solutionor in suspension. Optionally, the preparation may also be emulsified.The antigenic molecule may be mixed with excipients which arepharmaceutically acceptable and compatible with the active ingredient.Examples of favorable excipients are water, saline solution, dextrose,glycerol, ethanol or equivalents and their combinations. If desired, thevaccine may contain minor quantities of auxiliary substances such as“wetting” or emulsifying agents, pH buffering agents or adjuvants suchas aluminum hydroxide, muramyl dipeptide or variations thereof. In thecase of peptides, their coupling to a larger molecule (KLH, tetanustoxin) sometimes increases the immunogenicity. The vaccines areconventionally administered by injection, for example by subcutaneous orintramuscular injection. Additional formulations favorable with othermodes of administration include suppositories and sometimes oralformulations.

In general, the concentration of the polynucleotide in the compositionused for administration in vivo is from 0.1 μg/ml up to 20 mg/ml. Thepolynucleotide may be homologous or heterologous for the target cellinto which it will be introduced.

The present invention also relates to the use of vaccines includingmolecules of nucleic acids which encode the proteins of interest orimmunogenic peptides or their fragment(s), which are non-active,corresponding to the proteins of interest (SEQ ID No. 2, 4, 8, 9, 17 and24) and the peptide sequences or the fragments of said sequencesbelonging to the same family of proteins chosen from Perlecan, theprecursor of the retinol-binding plasma protein, GM2 activator protein,calgranulin B and saposin B (for example SEQ ID No. 1, SEQ ID No. 3, SEQID No. 5 to 7, SEQ ID No. 10 to 16, SEQ ID No. 18 to 23, SEQ ID No. 25to 29) and the peptide sequences which exhibit at least 70% identity,preferably at least 80% identity and advantageously at least 98%identity with any one of the peptide sequences SEQ ID No. 1 to 29. Thenucleic acid vaccines, in particular the DNA vaccines, are generallyadministered in association with a pharmaceutically acceptable vehicleby intramuscular injection.

From the amino acid sequence of the proteins of interest described (SEQID No. 2, 4, 8, 9, 17 and 24) and the peptide sequences or the fragmentsof said sequences belonging to the same family of proteins chosen fromPerlecan, the precursor of the retinol-binding plasma protein, GM2activator protein, calgranulin B and saposin B (for example SEQ ID No.1, SEQ ID No. 3, SEQ ID No. 5 to 7, SEQ ID No. 10 to 16, SEQ ID No. 18to 23, SEQ ID No. 25 to 29) and the peptide sequences which exhibit atleast 70% identity, preferably at least 80% identity and advantageouslyat least 98% identity with any one of the peptide sequences SEQ ID No. 1to 29, peptides or fragments corresponding to all or part of the primarysequence of these proteins may be synthesized by conventional methods ofpeptide synthesis or obtained by genetic recombination.

Recombinant proteins corresponding to the proteins of interest, producedin a prokaryotic or eukaryotic cellular system, are available fromvarious teams and are described in the literature. They may also beproduced by persons skilled in the art from the knowledge of thesequences of the corresponding genes described in the literature andtaking into account the degeneracy of the genetic code. All the proteinsequences identified in the present invention are thus capable of beingobtained by genetic recombination. The genes are cloned into suitablevectors. Different vectors are used to transform prokaryotic cells (forexample E. coli) and eukaryotic cells (for example COS cells, CHO cellsand Simliki cells). The recombinant proteins corresponding to theproteins of interest or to fragments of the proteins of interest maythus be produced in prokaryotic and/or eukaryotic cellular systems. InE. Coli cells, the recombinant proteins are produced with apolyhistidine tail. The insoluble protein fraction is solubilized in 8Murea. Enrichment of the product was carried out on nickel-chelated resin(Qiagen). The column was washed with decreasing concentrations of urea.The elution was carried out with imidazole in the absence of urea. Thecomplete sequence of the proteins of interest may also be cloned into asuitable plasmid and then transferred into the vaccinia virus in orderto obtain a recombinant virus.

Use of ligands capable of binding to the proteins of interest identifiedin the present invention.

The present invention relates to a biological material for thepreparation of pharmaceutical compositions for treating mammalssuffering from an autoimmune disease, preferably multiple sclerosis,comprising:

(i) either at least one ligand capable of binding to the proteins and/orfragments of the proteins chosen from the target proteins SEQ ID No. 2,4, 8, 9, 14 and 24 and the peptide sequences or the fragments of saidsequences belonging to the same family of proteins chosen from Perlecan,the precursor of the retinol-binding plasma protein, GM2 activatorprotein, calgranulin B and saposin B (for example SEQ ID No. 1, SEQ IDNo. 3, SEQ ID No. 5 to 7, SEQ ID No. 10 to 16, SEQ ID No. 18 to 23, SEQID No. 25 to 29) and the peptide sequences which exhibit at least 70%identity, preferably at least 80% identity and advantageously at least98% identity with any one of the peptide sequences SEQ ID No. 1 to 29,the ligand being capable or not of inhibiting the protein activity,(ii) or at least one polyclonal or monoclonal antibody capable ofbinding to at least one protein or one of its fragments chosen from thetarget proteins SEQ ID No. 2, 4, 8, 9, 14 and 24 and the peptidesequences or the fragments of said sequences belonging to the samefamily of proteins chosen from Perlecan, the precursor of theretinol-binding plasma protein, GM2 activator protein, calgranulin B andsaposin B (for example SEQ ID No. 1, SEQ ID No. 3, SEQ ID No. 5 to 7,SEQ ID No. 10 to 16, SEQ ID No. 18 to 23, SEQ ID No. 25 to 29) and thepeptide sequences which exhibit at least 70% identity, preferably atleast 80% identity and advantageously at least 98% identity with any oneof the peptide sequences SEQ ID No. 1 to 29. This antibody may beneutralizing or not, that is to say capable or not of inhibiting theactivity of the protein of interest. The ligand may be chosen from anymolecule or molecule fragment capable of binding to the target proteins,for example the receptor for this proteins, the cofactors for theseproteins, the polyclonal or monoclonal antibodies capable of binding tothe proteins or any fragment of these proteins.

These antibodies are very useful in particular for allowing the use oftherapeutic compositions because they lead, for example, to immunereactions directed specifically against immunodominant epitopes oragainst antigens exhibiting high variability. There are administered tothe patient either neutralizing soluble antibodies in order to inhibittheir function, or specific soluble antibodies in order to eliminate thepeptide by formation of immune complexes. The invention describes theuse of antibodies capable of specifically recognizing at least oneprotein described in the present invention for the treatment and/or forthe therapeutic monitoring of a degenerative and/or neurological and/orautoimmune disease, preferably multiple sclerosis. These antibodies arepolyclonal and preferably monoclonal. Preferably, these antibodiesrecognize the active site of the protein and, upon binding, inhibits thefunction of the protein. The capacity of the antibody to specificallybind to the protein is analyzed by conventional techniques which havebeen described, such as for example by ELISA or Western blot tests usingthe natural or synthetic immunogenic peptide or protein. The antibodytiter is determined. The capacity of the antibody to neutralize thefunction of the protein may be analyzed by various means, for example bydetermining the reduction in the activity of the immunogenic peptide orprotein in the presence of antibodies, preferably by determining thereduction in the gliotoxic activity using the bioassay test in vitro.

For example, the monoclonal antibodies directed against the targetprotein or a portion of this protein are produced by conventionaltechniques used to produce antibodies against surface antigens. Mice orrabbits are immunized (i) either with the natural or recombinant proteinof interest, (ii) or with any immunogenic peptide of this protein ofinterest, (iii) or with murine cells which express the protein or thepeptide of interest and the MHCII molecules.

The Balb/c murine line is the most frequently used. The immunogen isalso a peptide chosen from the peptides defined from the primarysequences of the proteins of interest. For example, the followingimmunogen was prepared: the peptides SEQ ID Nos. 58, 59, 60 derived fromthe sequence of the GM2 activator protein, the peptides SEQ ID Nos. 61,62 derived from the sequence of saposin B and the peptides SEQ ID Nos.63, 64, 65 derived from calgranulin B were coupled to Keyhole Lymphethemocyanin, abbreviated peptide-KLH, as support for its use inimmunization, or coupled to human serum albumin, abbreviatedpeptide-HSA. The animals were subjected to an injection of peptide-KLHor of peptide-HSA using complete Freund's adjuvant (CFA). The sera andthe hybridoma culture supernatants derived from animals immunized witheach peptide were analyzed for the presence of anti-protein antibodiesby an ELISA test using the initial proteins. The spleen cells of thesemice were consequently recovered and fused with myeloma cells.Polyethylene glycol (PEG) is the fusion agent most frequently used. Thehybridomas producing the most specific and the most sensitive antibodiesare selected. The monoclonal antibodies may be produced in vitro by cellculture of the hybridomas produced or by recovering murine ascitic fluidafter intraperitoneal injection of the hybridomas in mice. Whatever themode of production, in supernatant or in ascites, it is then importantto purify the monoclonal antibody. The methods of purification used areessentially ion-exchange gel filtration or exclusion chromatography, oreven immunoprecipitation. For each antibody, the method which will makeit possible to obtain the best yield should be chosen. A satisfactorynumber of anti-protein antibodies are targeted in functional tests inorder to identify the most efficient antibodies for binding the proteinof interest and/or for blocking the activity of the protein of interest.The monoclonal antibodies selected are humanized by standard “CDRgrafting” methods (protocol performed by many companies, as a service).These humanized antibodies may be clinically tested in the patient. Theefficiency of these antibodies may be monitored by clinical parameters.

The in vitro production of antibodies, of antibody fragments or ofantibody derivatives, such as chimeric antibodies, produced by geneticengineering, in eukaryotic cells has been described (EP 120 694 or EP125 023) and is also applicable to the present invention.

Use of molecules inhibiting the proteins of interest identified in thepresent invention.

The present invention relates to a biological material for thepreparation of pharmaceutical compositions for treating mammalssuffering from a degenerative and/or neurological and/or autoimmunedisease, preferably multiple sclerosis, said composition comprising (i)either at least one molecule inhibiting the function of at least oneprotein chosen from the proteins identified in the present invention(SEQ ID No. 2, 4, 8, 9, 17, 24) and the peptide sequences or thefragments of said sequences belonging to the same family of proteinschosen from Perlecan, the precursor of the retinol-binding plasmaprotein, GM2 activator protein, calgranulin B and saposin B (for exampleSEQ ID No. 1, SEQ ID No. 3, SEQ ID No. 5 to 7, SEQ ID No. 10 to 16, SEQID No. 18 to 23, SEQ ID No. 25 to 29) and the peptide sequences whichexhibit at least 70% identity, preferably at least 80% identity andadvantageously at least 98% identity with any one of the peptidesequences SEQ ID No. 1 to 29, for example inhibiting the gliotoxicactivity, (ii) or at least one molecule regulating the expression of atleast one protein chosen from the proteins SEQ ID No. 2, 4, 8, 9, 17, 24and the peptide sequences or the fragments of said sequences belongingto the same family of proteins chosen from Perlecan, the precursor ofthe retinol-binding plasma protein, GM2 activator protein, calgranulin Band saposin B (for example SEQ ID No. 1, SEQ ID No. 3, SEQ ID No. 5 to7, SEQ ID No. 10 to 16, SEQ ID No. 18 to 23, SEQ ID No. 25 to 29) andthe peptide sequences which exhibit at least 70% identity, preferably atleast 80% identity and advantageously at least 98% identity with any oneof the peptide sequences SEQ ID No. 1 to 29, for example to blocktranscription or translation, (iii) or at least one molecule regulatingthe metabolism of at least one protein chosen from the proteins SEQ IDNo. 2, 4, 8, 9, 17, 24 and the peptide sequences or the fragments ofsaid sequences belonging to the same family of proteins chosen fromPerlecan, the precursor of the retinol-binding plasma protein, GM2activator protein, calgranulin B and saposin B (for example SEQ ID No.1, SEQ ID No. 3, SEQ ID No. 5 to 7, SEQ ID No. 10 to 16, SEQ ID No. 18to 23, SEQ ID No. 25 to 29) and the peptide sequences which exhibit atleast 70% identity, preferably at least 80% identity and advantageouslyat least 98% identity with any one of the peptide sequences SEQ ID No. 1to 29, (iv) or at least one molecule regulating the expression and/orthe metabolism of a ligand for at least one protein chosen from theproteins SEQ ID No. 2, 4, 8, 9, 17, 24 and the peptide sequences or thefragments of said sequences belonging to the same family of proteinschosen from Perlecan, the precursor of the retinol-binding plasmaprotein, GM2 activator protein, calgranulin B and saposin B (for exampleSEQ ID No. 1, SEQ ID No. 3, SEQ ID No. 5 to 7, SEQ ID No. 10 to 16, SEQID No. 18 to 23, SEQ ID No. 25 to 29) and the peptide sequences whichexhibit at least 70% identity, preferably at least 80% identity andadvantageously at least 98% identity with any one of the peptidesequences SEQ ID No. 1 to SEQ ID No. 8 and SEQ ID No. 10 to 29 and thepeptide sequences which exhibit at least 70% identity, preferably atleast 80% identity and advantageously at least 98% identity with any oneof the peptide sequences SEQ ID No. 1 to 29, for example a receptor or acofactor. It is also possible to think that these proteins of the humanbody can be inhibited with no side effect.

Another important aspect of the invention relates to the identificationand the evaluation of the therapeutic efficacy of natural and/orsynthetic substances (i) capable of blocking and/or inhibiting theactivity of the proteins of interest of the invention and/or of theirfragment: SEQ ID No. 2, 4, 8, 9, 17, 24 and the peptide sequences or thefragments of said sequences belonging to the same family of proteinschosen from Perlecan, the precursor of the retinol-binding plasmaprotein, GM2 activator protein, calgranulin B and saposin B (for exampleSEQ ID No. 1, SEQ ID No. 3, SEQ ID No. 5 to 7, SEQ ID No. 10 to 16, SEQID No. 18 to 23, SEQ ID No. 25 to 29) and the peptide sequences whichexhibit at least 70% identity, preferably at least 80% identity andadvantageously at least 98% identity with any one of the peptidesequences SEQ ID No. 1 to 29 and/or (ii) capable of inhibiting theirmetabolism such as the inhibitors of the corresponding metabolism, theinhibitors of enzymes activated by the coenzymes, (iii) capable ofregulating the expression of the proteins of interest (SEQ ID No. 2, 4,8, 9, 17, 24 and the peptide sequences or the fragments of saidsequences belonging to the same family of proteins chosen from Perlecan,the precursor of the retinol-binding plasma protein, GM2 activatorprotein, calgranulin B and saposin B (for example SEQ ID No. 1, SEQ IDNo. 3, SEQ ID No. 5 to 7, SEQ ID No. 10 to 16, SEQ ID No. 18 to 23, SEQID No. 25 to 29) and the peptide sequences which exhibit at least 70%identity, preferably at least 80% identity and advantageously at least98% identity with any one of the peptide sequences SEQ ID No. 1 to 29,(iv) capable of inhibiting the function and/or the expression of theligands for the proteins of interest SEQ ID No. 2, 4, 8, 9, 17, 24 andthe peptide sequences or the fragments of said sequences belonging tothe same family of proteins chosen from Perlecan, the precursor of theretinol-binding plasma protein, GM2 activator protein, calgranulin B andsaposin B (for example SEQ ID No. 1, SEQ ID No. 3, SEQ ID No. 5 to 7,SEQ ID No. 10 to 16, SEQ ID No. 18 to 23, SEQ ID No. 25 to 29) and thepeptide sequences which exhibit at least 70% identity, preferably atleast 80% identity and advantageously at least 98% identity with any oneof the peptide sequences SEQ ID No. 1 to 29, such as for examplereceptors. These substances may be used in prophylactic or therapeutictreatments of the disease. The invention also relates to methods fortreating and preventing an autoimmune disease, for example MS, byadministering effective quantities of these substances. The substancesmay be proteins, antibodies, small synthetic or natural molecules,derivatives of the proteins identified in this invention, lipids,glycolipids and the like. The small molecules may be screened andidentified in a large quantity using chemical combinatory libraries. Theinvention also relates to pharmaceutical compositions comprising thesesubstances in association with acceptable physiological carriers, andmethods for the preparation of medicaments to be used in the therapy orin the prevention of autoimmune diseases including MS using thesesubstances.

To identify inhibitory molecules of low molecular weight such ascandidate drugs for degenerative and/or neurological and/or autoimmunediseases, such as multiple sclerosis, there are used the tests andprotocols described in above and in the patent applications incorporatedby way of reference, using samples collected from untreated or treatedpatients, untreated or treated animal models, or tissues of untreated ortreated animal models. This aspect of the invention also includes amethod for identifying substances capable of blocking or inhibiting theactivity of the proteins of interest, comprising the introduction ofthese substances into a test in vitro or into an animal model in vivo.The molecules selected are tested at different concentrations. Theseinhibitors are also tested in toxicity and pharmaco-kinetic assays toknow if they can represent valid candidate drugs. The substances testedfor the inhibition or the blocking of the protein activities or for theexpression of the proteins, in these screening procedures, may beproteins, antibodies, antibody fragments, small synthetic or naturalmolecules, derivatives of the proteins of interest and the like. Thesmall molecules may be screened and identified in a large quantity usingchemical combinatory libraries.

By way of example, there may be mentioned as inhibitory substances:

The inhibitors of the proteins identified in the present invention (SEQID No. 2, 4, 8, 9, 17, 24), the peptide sequences or the fragments ofsaid sequences belonging to the same family of proteins chosen fromPerlecan, the precursor of the retinol-binding plasma protein, GM2activator protein, calgranulin B and saposin B (for example SEQ ID No.1, SEQ ID No. 3, SEQ ID No. 5 to 7, SEQ ID No. 10 to 16, SEQ ID No. 18to 23, SEQ ID No. 25 to 29) and the peptide sequences which exhibit atleast 70% identity, preferably at least 80% identity and advantageouslyat least 98% identity with any one of the peptide sequences SEQ ID No. 1to 29, and the inhibitors of the fragments of said proteins. Theseinhibitors may be included in a prophylactic and therapeuticcomposition, in particular for the treatment of multiple sclerosis. Forexample, lycorine, an alkaloid extracted from Amaryllidaceae (e.g.:Crinum asiaticum) is used in vitro at a concentration of between 0.1 and0.5 μg/ml and in vivo at a concentration of between 0.1 and 1 mg/kg/day.For example, Rolipram (trade name) and Ibudilast (trade name), which aretwo molecules of the same family of inhibitors of 4 (PDE4)phosphodiesterases, are used in vitro at concentrations of between 1 and10 μM/1 and in vivo at concentrations of between 10 mg/kg/day.

From the amino acid sequences of the proteins SEQ ID No. 2, 4, 8, 9, 17,24 and the peptide sequences or the fragments of said sequencesbelonging to the same family of proteins chosen from Perlecan, theprecursor of the retinol-binding plasma protein, GM2 activator protein,calgranulin B and saposin B (for example SEQ ID No. 1, SEQ ID No. 3, SEQID No. 5 to 7, SEQ ID No. 10 to 16, SEQ ID No. 18 to 23, SEQ ID No. 25to 29), it is evident that it is possible to deduce the DNA and RNAnucleotide sequences (SEQ ID No. 30, 31, 42, 53) corresponding to theproteins of interest and the sequences encoding the proteins of thefamily of these proteins of interest (for example SEQ ID No. 32 to 41,SEQ ID No. 43 to 52, SEQ ID No. 54 to 57, SEQ ID No. 66 to 67), takinginto account the genetic code and its degeneracy. Thus, the presentinvention relates to the use of these nucleotide sequences in the form:

of antisense sequences,

of sequences encoding a therapeutic gene,

of sequences which may be contained in a vector for carrying out celltransformation ex vitro and/or in vivo (gene therapy).

Use of nucleic acids deduced from the amino acid sequences of theproteins of interest identified in the present invention; antisensenucleic acids and/or nucleic acids encoding a therapeutic gene.

The present invention relates to a biological material for thepreparation of pharmaceutical compositions for treating mammalssuffering from a degenerative and/or neurological and/or autoimmunedisease, in particular multiple sclerosis, the composition comprising(i) either at least one nucleic acid sequence capable of hybridizingwith a nucleic acid sequence encoding the proteins of interest (SEQ IDNo. 2, 4, 8, 9, 17, 24) and the peptide sequences or the fragments ofsaid sequences belonging to the same family of proteins chosen fromPerlecan, the precursor of the retinol-binding plasma protein, GM2activator protein, calgranulin B and saposin B (for example SEQ ID No.1, SEQ ID No. 3, SEQ ID No. 5 to 7, SEQ ID No. 10 to 16, SEQ ID No. 18to 23, SEQ ID No. 25 to 29) and the peptide sequences which exhibit atleast 70% identity, preferably at least 80% identity and advantageouslyat least 98% identity with any one of the peptide sequences SEQ ID No. 1to 29, or their fragment(s), (ii) or at least one nucleic acid sequencecomprising at least one gene of therapeutic interest encoding theproteins or a fragment of proteins (SEQ ID No. 2, 4, 8, 9, 17, 24), thepeptide sequences or the fragments of said sequences belonging to thesame family of proteins chosen from Perlecan, the precursor of theretinol-binding plasma protein, GM2 activator protein, calgranulin B andsaposin B (for example SEQ ID No. 1, SEQ ID No. 3, SEQ ID No. 5 to 7,SEQ ID No. 10 to 16, SEQ ID No. 18 to 23, SEQ ID No. 25 to 29) and thepeptide sequences which exhibit at least 70% identity, preferably atleast 80% identity and advantageously at least 98% identity with any oneof the peptide sequences SEQ ID No. 1 to 29, and elements ensuring theexpression of said gene in vivo in target cells intended to begenetically modified by said nucleic sequence.

The expression nucleic acid sequence is understood to mean a DNA and/orRNA fragment which is double-stranded or single-stranded, linear orcircular, natural and isolated or synthetic, designating a precisesuccession of nucleotides, modified or otherwise, which makes itpossible to define a fragment or a region of a nucleic acid chosen fromthe group consisting of a cDNA; a genomic DNA; a plasmid DNA; amessenger RNA. These nucleic acid sequences are deduced from the aminoacid sequence of the proteins SEQ ID No. 2, 4, 8, 9, 17, 24 and thepeptide sequences or the fragments of said sequences belonging to thesame family of proteins chosen from Perlecan, the precursor of theretinol-binding plasma protein, GM2 activator protein, calgranulin B andsaposin B (for example SEQ ID No. 1, SEQ ID No. 3, SEQ ID No. 5 to 7,SEQ ID No. 10 to 16, SEQ ID No. 18 to 23, SEQ ID No. 25 to 29) and thepeptide sequences which exhibit at least 70% identity, preferably atleast 80% identity and advantageously at least 98% identity with any oneof the peptide sequences SEQ ID No. 1 to 29, using the genetic code.Because of the degeneracy of the genetic code, the invention alsoencompasses equivalent or homologous sequences. These defined sequencesallow persons skilled in the art themselves to define the appropriatenucleic acids.

Accordingly, the present invention relates to a biological material forthe preparation of pharmaceutical compositions comprising at least onenucleic acid sequence capable of hybridizing with a nucleic acidsequence encoding the proteins of interest or their fragment(s) (SEQ IDNo. 2, 4, 8, 9, 17, 24) and the peptide sequences or the fragments ofsaid sequences belonging to the same family of proteins chosen fromPerlecan, the precursor of the retinol-binding plasma protein, GM2activator protein, calgranulin B and saposin B (for example SEQ ID No.1, SEQ ID No. 3, SEQ ID No. 5 to 7, SEQ ID No. 10 to 16, SEQ ID No. 18to 23, SEQ ID No. 25 to 29) and the peptide sequences which exhibit atleast 70% identity, preferably at least 80% identity and advantageouslyat least 98% identity with any one of the peptide sequences SEQ ID No. 1to 29.

The invention consists in defining and using nucleic acid moleculescomplementary to the DNA and/or RNA sequences encoding the proteins ofinterest or their fragment(s). These fragments correspond to ribozyme orantisense molecules and may be synthesized using automated synthesizers,such as those marketed by the company Applied Biosystem. The inventiondescribes the use of these nucleic acids capable of hybridizing understringent conditions with the DNA and/or RNA encoding the proteins ofthe invention or their fragment(s). Characteristic stringency conditionsare those which correspond to a combination of the temperature and ofthe saline concentration chosen approximately between 12 and 20° C.under the Tm (“melting temperature”) of the hybrid under study. Suchmolecules are synthesized and may be labeled using conventional labelingmethods used for molecular probes, or may be used as primers inamplification reactions. The sequences which exhibit at least 90%homology relative to a reference sequence also form part of theinvention, as well as the fragments of these sequences which have atleast 20 nucleotides and preferably 30 contiguous nucleotides that arehomologous with respect to a reference sequence. To reduce theproportion of natural or variant peptides, it is possible to envisage anantisense and/or ribozyme approach. Such an approach is widely describedin the literature. Of course, such antisense molecules may constitute,as such, vectors. It is also possible to use vectors which comprise anucleic acid sequence which encodes an antisense.

The present invention relates to a biological material for thepreparation of pharmaceutical compositions for treating mammalssuffering from a degenerative and/or neurological and/or autoimmunedisease, such as multiple sclerosis, said composition comprising atleast one nucleic acid sequence containing at least one gene oftherapeutic interest and elements ensuring the expression of said genein vivo in target cells intended to be genetically modified by saidnucleic sequence.

These nucleic acid sequences and/or vectors (antisense or encoding aprotein or a fragment of a protein) make it possible to target the cellsin which the peptide is expressed, such as macrophage cells: (i) eitherby the use of a targeting molecule introduced on the vector, (ii) or bythe use of a particular property of these cells.

Use of vectors comprising a gene of therapeutic interest correspondingto the genes for the proteins of interest identified in the presentinvention.

The present invention relates to a biological material for thepreparation of pharmaceutical compositions for preventing and treatingdegenerative and/or neurological and/or autoimmune diseases, such asmultiple sclerosis, the composition comprising a nucleic acid sequencecomprising a gene of therapeutic interest and elements for expressingsaid gene of interest. The genes may be nonmutated or mutated. They mayalso consist of nucleic acids modified such that it is not possible forthem to integrate into the genome of the target cell, or of nucleicacids stabilized with the aid of agents, such as spermine.

Such a gene of therapeutic interest encodes in particular:

(i) either at least one protein chosen from the proteins identified inthe present invention (SEQ ID No. 2, 4, 8, 9, 17, 24) and the peptidesequences or the fragments of said sequences belonging to the samefamily of proteins chosen from Perlecan, the precursor of theretinol-binding plasma protein, GM2 activator protein, calgranulin B andsaposin B (for example SEQ ID No. 1, SEQ ID No. 3, SEQ ID No. 5 to 7,SEQ ID No. 10 to 16, SEQ ID No. 18 to 23, SEQ ID No. 25 to 29) and thepeptide sequences which exhibit at least 70% identity, preferably atleast 80% identity and advantageously at least 98% identity with any oneof the peptide sequences SEQ ID No. 1 to 29, or their fragment(s),(ii) or at least all or part of a polyclonal or mono-clonal antibodycapable of binding to at least one protein or a protein fragment chosenfrom the proteins identified in the present invention (SEQ ID No. 2, 4,8, 9, 17, 24) and the peptide sequences or the fragments of saidsequences belonging to the same family of proteins chosen from Perlecan,the precursor of the retinol-binding plasma protein, GM2 activatorprotein, calgranulin B and saposin B (for example SEQ ID No. 1, SEQ IDNo. 3, SEQ ID No. 5 to 7, SEQ ID No. 10 to 16, SEQ ID No. 18 to 23, SEQID No. 25 to 29) and the peptide sequences which exhibit at least 70%identity, preferably at least 80% identity and advantageously at least98% identity with any one of the peptide sequences SEQ ID No. 1 to 29.This may include in particular a native transmembrane antibody, or afragment or derivative of such an antibody, as long as said antibody,antibody fragment or derivative is expressed at the surface of thegenetically modified target cell of the mammal and is capable of bindingto a polypeptide present at the surface of a cytotoxic effector cell orof a helper T lymphocyte involved in the process for activating such acell,(iii) or at least one molecule inhibiting at least one protein or itsfragments, said protein being chosen from the proteins identified (SEQID No. 2, 4, 8, 9, 17, 24) and the peptide sequences or the fragments ofsaid sequences belonging to the same family of proteins chosen fromPerlecan, the precursor of the retinol-binding plasma protein, GM2activator protein, calgranulin B and saposin B (for example SEQ ID No.1, SEQ ID No. 3, SEQ ID No. 5 to 7, SEQ ID No. 10 to 16, SEQ ID No. 18to 23, SEQ ID No. 25 to 29) and the peptide sequences which exhibit atleast 70% identity, preferably at least 80% identity and advantageouslyat least 98% identity with any one of the peptide sequences SEQ ID No. 1to 29; the proteins inhibiting the function and/or the metabolism and/orthe binding of the proteins SEQ ID No. 2, 4, 8, 9, 17, 24 and thepeptide sequences or the fragments of said sequences belonging to thesame family of proteins chosen from Perlecan, the precursor of theretinol-binding plasma protein, GM2 activator protein, calgranulin B andsaposin B (for example SEQ ID No. 1, SEQ ID No. 3, SEQ ID No. 5 to 7,SEQ ID No. 10 to 16, SEQ ID No. 18 to 23, SEQ ID No. 25 to 29) and thepeptide sequences which exhibit at least 70% identity, preferably atleast 80% identity and advantageously at least 98% identity with any oneof the peptide sequences SEQ ID No. 1 to 29,(iv) or at least one ligand or any portion of a ligand capable ofbinding to at least one protein or one protein fragment chosen from theproteins identified (SEQ ID No. 2, 4, 8, 9, 17, 24) and the peptidesequences or the fragments of said sequences belonging to the samefamily of proteins chosen from Perlecan, the precursor of theretinol-binding plasma protein, GM2 activator protein, calgranulin B andsaposin B (for example SEQ ID No. 1, SEQ ID No. 3, SEQ ID No. 5 to 7,SEQ ID No. 10 to 16, SEQ ID No. 18 to 23, SEQ ID No. 25 to 29) and thepeptide sequences which exhibit at least 70% identity, preferably atleast 80% identity and advantageously at least 98% identity with any oneof the peptide sequences SEQ ID No. 1 to 29, and/or of inhibiting itsfunction.

More particularly, the expression antibody fragment is understood tomean the F(ab)2, Fab′, Fab, sFv fragments (Blazar et al., 1997, Journalof Immunology 159: 5821–5833; Bird et al., 1988 Science 242: 423–426) ofa native antibody and the expression derivative is understood to mean,for example, a chimeric derivative of such an antibody (see for examplethe chimeras of the Mouse/Human anti-CD3 antibodies in Arakawa et al.,1996 J Biochem 120: 657–662 or the immunotoxins such as sFv-toxin byChaudary et al 1989, Nature 339: 394–397). The expression transmembraneantibody is understood to mean an antibody in which at least thefunctional region capable of recognizing and binding to its specificantigen is expressed at the surface of the target cells in order toallow said recognition and binding. More particularly, the antibodiesaccording to the present invention consist of fusion polypeptidescomprising the amino acids defining said functional region and an aminoacid sequence (transmembrane polypeptide) allowing anchoring within themembrane lipid double layer of the target cell or at the outer surfaceof this bilayer. The nucleic sequences encoding numerous transmembranepolypeptides are described in the literature. According to a mostadvantageous case, the nucleic acid sequence encoding the antibody heavychain is fused with the nucleic acid sequence encoding the saidtransmembrane polypeptide.

The expression elements ensuring the expression of said gene in vivorefers in particular to the elements necessary to ensure the expressionof said gene after its transfer into a target cell. This includes inparticular promoter sequences and/or regulatory sequences which areefficient in said cell, and optionally the sequences required to allowexpression at the surface of the target cells of said polypeptide. Thepromoter used may be a viral, ubiquitous or tissue-specific promoter ora synthetic promoter. By way of example, there may be mentionedpromoters such as the promoters of the viruses RSV (Rous Sarcoma Virus),MPSV, SV40 (Simian Virus), CMV (Cytomegalovirus) or of the vacciniavirus, the promoters of the gene encoding muscle creatine kinase, actin.It is, in addition, possible to choose a promoter sequence specific fora given cell type, or activable under defined conditions. The literatureprovides a large amount of information relating to such promotersequences.

Moreover, said nucleic acid may comprise at least two sequences, whichare identical or different, exhibiting a transcriptional promoteractivity and/or at least two genes, which are identical or different,situated relative to each other contiguously, apart, in the samedirection or in the opposite direction, provided that thetranscriptional promoter function or the transcription of said genes isnot affected.

Likewise, in this type of nucleic acid construct, it is possible tointroduce “neutral” nucleic sequences or introns which do not adverselyaffect the transcription and are spliced before the translational step.Such sequences and their uses are described in the literature(reference: PCT patent application WO 94/29471).

Said nucleic acid may also comprise sequences required for intracellulartransport, for replication and/or for integration, for transcriptionand/or translation. Such sequences are well known to persons skilled inthe art.

Moreover, the nucleic acids which can be used according to the presentinvention may also be nucleic acids modified such that it is notpossible for them to integrate into the genome of the target cell ornucleic acids stabilized with the aid of agents, such as, for example,spermine, which, as such, have no effect on the efficiency of thetransfection.

According to one embodiment of the invention, the nucleic acid sequenceis a naked RNA or DNA sequence, that is to say which is free of anycompound facilitating its introduction into cells (transfer of nucleicacid sequence). However, according to a second embodiment of theinvention, to promote its introduction into the target cells and toobtain the genetically modified cells of the invention, this nucleicacid sequence may be in the form of a “vector” and more particularly inthe form of a viral vector, such as, for example, an adenoviral vector,a retroviral vector, a vector derived from a poxvirus, in particularderived from the vaccinia virus or from the Modified Virus Ankara (MVA)or from a nonviral vector such as, for example, a vector consisting ofat least one said nucleic acid sequence complexed or conjugated with atleast one carrier molecular substance selected from the group consistingof a cationic amphiphile, in particular a cationic lipid, a cationic orneutral polymer, a practical polar compound chosen in particular frompropylene glycol, polyethylene glycol, glycerol, ethanol,1-methyl-L-2-pyrrolidone or their derivatives, and an aprotic polarcompound chosen in particular from dimethyl sulfoxide (DMSO), diethylsulfoxide, di-n-propyl sulfoxide, dimethyl sulfone, sulfolane,dimethylformamide, dimethylacetamide, tetramethylurea, acetonitrile ortheir derivatives. The literature provides a large number of examples ofsuch viral and nonviral vectors.

Such vectors may in addition and preferably comprise targeting elementswhich can make it possible to direct the transfer of a nucleic acidsequence toward certain cell types or certain particular tissues such ascyto-toxic cells and antigen-presenting cells). They can also make itpossible to direct the transfer of an active substance toward certainpreferred intracellular compartments such as the nucleus, themitochondria or the peroxisomes, for example. This may also includeelements facilitating penetration into the cell or the lysis ofintracellular compartments. Such targeting elements are widely describedin the literature. This may include, for example, all or part oflectins, peptides, in particular the peptide JTS-1 (see PCT patentapplication WO 94/40958), oligonucleotides, lipids, hormones, vitamins,antigens, antibodies, ligands specific to membrane receptors, ligandscapable of acting with an antiligand, fusogenic peptides, nuclearlocalization peptides or a composition of such compounds.

Use of cells transformed in vivo after injection of vectors containingat least one gene of therapeutic interest defined from the proteins ofinterest identified in the present invention (SEQ ID No. 2, 4, 8, 9, 17,24) and the peptide sequences or the fragments of said sequencesbelonging to the same family of proteins chosen from Perlecan, theprecursor of the retinol-binding plasma protein, GM2 activator protein,calgranulin B and saposin B (for example SEQ ID No. 1, SEQ ID No. 3, SEQID No. 5 to 7, SEQ ID No. 10 to 16, SEQ ID No. 18 to 23, SEQ ID No. 25to 29) and the peptide sequences which exhibit at least 70% identity,preferably at least 80% identity and advantageously at least 98%identity with any one of the peptide sequences SEQ ID No. 1 to 29.

The present invention relates to a biological material for thepreparation of pharmaceutical compositions for preventing and treatingmammals suffering from degenerative and/or neurological and/orautoimmune diseases, preferably multiple sclerosis, the compositioncomprising at least one vector containing a therapeutic gene asdescribed below, capable of being introduced into a target cell in vivoand of expressing the gene of therapeutic interest in vivo. Theadvantage of this invention consists in the possibility of maintaininglong term a basal level of molecules expressed in the patient treated.Vectors or nucleic acids encoding genes of therapeutic interest areinjected. These vectors and nucleic acids should be transported up tothe target cells and transfect these cells in which they have to beexpressed in vivo.

The invention relates to the expression in vivo of nucleotide sequencesand/or vectors as designated in the preceding paragraph, that is to saysequences corresponding to genes of therapeutic interest encoding inparticular:

(i) either at least one protein chosen from the proteins identified inthe present invention (SEQ ID No. 2, 4, 8, 9, 17, 24) and the peptidesequences or the fragments of said sequences belonging to the samefamily of proteins chosen from Perlecan, the precursor of theretinol-binding plasma protein, GM2 activator protein, calgranulin B andsaposin B (for example SEQ ID No. 1, SEQ ID No. 3, SEQ ID No. 5 to 7,SEQ ID No. 10 to 16, SEQ ID No. 18 to 23, SEQ ID No. 25 to 29) and thepeptide sequences which exhibit at least 70% identity, preferably atleast 80% identity and advantageously at least 98% identity with any oneof the peptide sequences SEQ ID No. 1 to 29, or their fragment(s),(i) or at least all or part of a polyclonal or mono-clonal antibodycapable of binding to at least one protein chosen from the proteinsidentified in the present invention (SEQ ID No. 2, 4, 8, 9, 17, 24) andthe peptide sequences or the fragments of said sequences belonging tothe same family of proteins chosen from Perlecan, the precursor of theretinol-binding plasma protein, GM2 activator protein, calgranulin B andsaposin B (for example SEQ ID No. 1, SEQ ID No. 3, SEQ ID No. 5 to 7,SEQ ID No. 10 to 16, SEQ ID No. 18 to 23, SEQ ID No. 25 to 29) and thepeptide sequences which exhibit at least 70% identity, preferably atleast 80% identity and advantageously at least 98% identity with any oneof the peptide sequences SEQ ID No. 1 to 29. This may include a nativetransmembrane antibody, or a fragment or derivative of such an antibody,as long as said antibody or antibody fragment or derivative is expressedat the surface of the genetically modified target mammalian cell and inthat said antibody is capable of binding to a polypeptide present at thesurface of a cytotoxic effector cell or of a helper T lymphocyte andinvolved in the process of activating such a cell. This may includeantibody fragments expressed by cells capable of secreting saidantibodies in the bloodstream of a mammal or patient carrying the cellsgenetically modified by the gene encoding the antibody,(ii) or at least one molecule inhibiting at least one protein chosenfrom the proteins identified (SEQ ID No. 2, 4, 8, 9, 17, 24) and thepeptide sequences or the fragments of said sequences belonging to thesame family of proteins chosen from Perlecan, the precursor of theretinol-binding plasma protein, GM2 activator protein, calgranulin B andsaposin B (for example SEQ ID No. 1, SEQ ID No. 3, SEQ ID No. 5 to 7,SEQ ID No. 10 to 16, SEQ ID No. 18 to 23, SEQ ID No. 25 to 29) and thepeptide sequences which exhibit at least 70% identity, preferably atleast 80% identity and advantageously at least 98% identity with any oneof the peptide sequences SEQ ID No. 1 to 29; protein inhibiting thefunction and/or metabolism and/or binding of the proteins SEQ ID No. 2,4, 8, 9, 17, 24 and the peptide sequences or the fragments of saidsequences belonging to the same family of proteins chosen from Perlecan,the precursor of the retinol-binding plasma protein, GM2 activatorprotein, calgranulin B and saposin B (for example SEQ ID No. 1, SEQ IDNo. 3, SEQ ID No. 5 to 7, SEQ ID No. 10 to 16, SEQ ID No. 18 to 23, SEQID No. 25 to 29) and the peptide sequences which exhibit at least 70%identity, preferably at least 80% identity and advantageously at least98% identity with any one of the peptide sequences SEQ ID No. 1 to 29,(iii) or at least one ligand or any portion of the ligand capable ofbinding to at least one protein chosen from the proteins identified (SEQID No. 2, 4, 8, 9, 17, 24) and the peptide sequences or the fragments ofsaid sequences belonging to the same family of proteins chosen fromPerlecan, the precursor of the retinol-binding plasma protein, GM2activator protein, calgranulin B and saposin B (for example SEQ ID No.1, SEQ ID No. 3, SEQ ID No. 5 to 7, SEQ ID No. 10 to 16, SEQ ID No. 18to 23, SEQ ID No. 25 to 29) and the peptide sequences which exhibit atleast 70% identity, preferably at least 80% identity and advantageouslyat least 98% identity with any one of the peptide sequences SEQ ID No. 1to 29, and/or of inhibiting its function.

According to a particular embodiment, this includes using gene therapyso as to direct the immune response against the target protein, peptideor molecule of interest, that is to say against any protein chosen fromthe proteins SEQ ID No. 2, 4, 8, 9, 17, 24 and the peptide sequences orthe fragments of said sequences belonging to the same family of proteinschosen from Perlecan, the precursor of the retinol-binding plasmaprotein, GM2 activator protein, calgranulin B and saposin B (for exampleSEQ ID No. 1, SEQ ID No. 3, SEQ ID No. 5 to 7, SEQ ID No. 10 to 16, SEQID No. 18 to 23, SEQ ID No. 25 to 29) and the peptide sequences whichexhibit at least 70% identity, preferably at least 80% identity andadvantageously at least 98% identity with any one of the peptidesequences SEQ ID No. 1 to 29, their fragment(s) and/or against anymolecule inhibiting the function and/or expression and/or metabolism ofsaid proteins of interest, and/or ligands of said proteins such as, forexample, the receptors. For that, it is evident that the cells to betargeted for the transformation with a vector are cells belonging to theimmune system, either lymphocyte-type cells (CD4/CD8), orantigen-presenting cells (dendritic cells, macrophages and the like).

According to a particular embodiment, the antigen-presenting cells (APC)are genetically modified, in particular in vivo. APCs such asmacrophages, dendritic cells, microgliocytes and astrocytes play a rolein initiating the immune response. They are the first cellularcomponents which capture the antigen, prepare it in the cell and expressthe transmembrane MHCI and MHCII molecules involved in presenting theimmunogen to the CD4+ and CD8+ T cells, they produce specific secondaryproteins which participate in activating the T cells (Debrick et al.,1991, J. Immunol 147: 2846; Reis et al., 1993, J Ep Med 178: 509;Kovacsovics-bankowski et al., 1993, PNAS 90: 4942; Kovacsovics-bankowskiet al., 1995 Science 267: 243; Svensson et al., 1997, J Immunol 158:4229; Norbury et al., 1997, Eur J Immunol 27: 280). For a vaccination,it may be advantageous to have a gene therapy system which can targetthe gene transfer into such APC cells, that is to say a gene whichencodes a polypeptide which can, after its intracellular production andits “processing”, be presented to the CD8+ and/or CD4+ cells by themolecules of the MHCI and MHCII complexes, respectively, at the surfaceof these cells.

It is chosen to express at the surface of the APC cells in vivo all orpart of an antibody and/or of a ligand such as, for example, a receptor,capable of reacting with the target protein or peptide chosen from theproteins SEQ ID No. 2, 4, 8, 9, 17, 24 and the peptide sequences or thefragments of said sequences belonging to the same family of proteinschosen from Perlecan, the precursor of the retinol-binding plasmaprotein, GM2 activator protein, calgranulin B and saposin B (for exampleSEQ ID No. 1, SEQ ID No. 3, SEQ ID No. 5 to 7, SEQ ID No. 10 to 16, SEQID No. 18 to 23, SEQ ID No. 25 to 29) and the peptide sequences whichexhibit at least 70% identity, preferably at least 80% identity andadvantageously at least 98% identity with any one of the peptidesequences SEQ ID No. 1 to 29. Such cells will then specificallyphagocytose said protein or said peptide, the “processer” so thatfragments of this peptide are present at the surface of theantigen-presenting cells.

The literature provides a large number of examples of genes encodingantibodies capable of reacting with polypeptides or receptors. It iswithin the capability of persons skilled in the art to obtain thenucleic acid sequences encoding such antibodies. There may be mentioned,for example, the genes encoding the light and heavy chains of theantibody YTH 12.5 (anti-CD3) (Routledge et al. 1991, Eur J Immunol 21:2717–2725), of the anti-CD3 according to Arakawa et al; 1996, J.Biochem. 120: 657–662. The nucleic acid sequences of such antibodies areeasily identifiable from the databases commonly used by persons skilledin the art. It is also possible, starting with hybridomas available fromATCC, to clone the nucleic acid sequences encoding the heavy and/orlight chains of these various antibodies by amplification methods suchas RT-PCR with the aid of specific oligonucleotides or techniques usingcDNA libraries (Maniatis et al., 1982, Molecular cloning. A laboratorymanual CSH Laboratory, Cold Spring Harbor, N.Y.). The sequences thuscloned are then available for their cloning into vectors. According to apreferred case of the invention, the nucleic acid sequence encoding theheavy chain of the antibody is fused by homologous recombination withthe nucleic acid sequence encoding a transmembrane polypeptide such asthe rabies glycoprotein or gp160 (Polydefkis et al., 1990, J Exp Med171: 875–887). These molecular biology techniques have been fullydescribed.

It is chosen to express at the surface of the APC cells in vivoimmunogenic fragments corresponding to at least one proteins chosen fromthe proteins SEQ ID No. 2, 4, 8, 9, 17, 24 and the peptide sequences orthe fragments of said sequences belonging to the same family of proteinschosen from Perlecan, the precursor of the retinol-binding plasmaprotein, GM2 activator protein, calgranulin B and saposin B (for exampleSEQ ID No. 1, SEQ ID No. 3, SEQ ID No. 5 to 7, SEQ ID No. 10 to 16, SEQID No. 18 to 23, SEQ ID No. 25 to 29) and the peptide sequences whichexhibit at least 70% identity, preferably at least 80% identity andadvantageously at least 98% identity with any one of the peptidesequences SEQ ID No. 1 to 29. For that, it is possible to choose tocause the vector to express either the full-length polypeptide or,preferably, polypeptides selected to react with specific ligands and/orreceptors. The immunogenic peptide encoded by the polynucleotideintroduced into the cell of the vertebrate in vivo may be producedand/or secreted, made ready and then presented to an antigen-presentingcell (APC) in the context of the molecules of the MHC.

The APCs thus transferred in vivo induce an immune response directedagainst the immunogen expressed in vivo. The APCs possess differentmechanisms for capturing the antigens: (a) capture of the antigens bymembrane receptors such as the receptors for immuno-globulins (Fc) orfor the complement which are available at the surface of thegranulocytes, monocytes or macrophages allowing efficient delivery ofthe antigen into the intracellular compartments after phagocytosismediated by the receptors. (b) entry into the APCs by pinocytosis influid phase, involving various mechanisms: micropinocytosis, that is tosay the capture of small vesicles (0.1 μm) by the clathrin-coated pits,and macropinocytosis, that is to say the capture of larger vesicles(with a size varying graft 0.5 μm and about 6 μm) (Sallusto et al. 1995,J Exp Med 182: 389–400). While micropinocytosis constitutively exists inall cells, macropinocytosis is limited to cellular types such as, forexample, the macrophages, dendritic cells, astrocytes, epithelial cellsstimulated by growth factors (Racoosin et al., J Cell Sci 1992, 102:867–880). In this invention, the expression cells capable ofmacropinocytosis is understood to mean the cells which can carry out theevents described above and the cells which can capture macromoleculespreferably between 0.5 μm and about 6 μm in the cytoplasm.

According to a particular embodiment, the cytotoxic effector cells orthe helper T lymphocytes are genetically modified in particular in vivoso that they express at their surface a polypeptide corresponding to theproteins SEQ ID No. 2, 4, 8, 9, 17, 24 and the peptide sequences or thefragments of said sequences belonging to the same family of proteinschosen from Perlecan, the precursor of the retinol-binding plasmaprotein, GM2 activator protein, calgranulin B and saposin B (for exampleSEQ ID No. 1, SEQ ID No. 3, SEQ ID No. 5 to 7, SEQ ID No. 10 to 16, SEQID No. 18 to 23, SEQ ID No. 25 to 29) and the peptide sequences whichexhibit at least 70% identity, preferably at least 80% identity andadvantageously at least 98% identity with any one of the peptidesequences SEQ ID No. 1 to 29, ligands for said proteins, which arenaturally not expressed by these cells and which are capable of inducingthe process of activation of such cells, by introducing into these cellsnucleic acid sequences containing the gene encoding such a polypeptide.In accordance with the present invention, it is also possible to selecta nucleic acid sequence containing a gene of therapeutic interestencoding all or part of an antibody directed against a protein chosenfrom the proteins SEQ ID No. 2, 4, 8, 9, 17, 24 and the peptidesequences or the fragments of said sequences belonging to the samefamily of proteins chosen from Perlecan, the precursor of theretinol-binding plasma protein, GM2 activator protein, calgranulin B andsaposin B (for example SEQ ID No. 1, SEQ ID No. 3, SEQ ID No. 5 to 7,SEQ ID No. 10 to 16, SEQ ID No. 18 to 23, SEQ ID No. 25 to 29) and thepeptide sequences which exhibit at least 70% identity, preferably atleast 80% identity and advantageously at least 98% identity with any oneof the peptide sequences SEQ ID No. 1 to 29, capable of being expressedat the surface of the target cells of the patient to be treated, saidantibody being capable of binding to a polypeptide which is naturallynot expressed by these cytotoxic effector cells or helper T lymphocytes.

The expression cytotoxic effector cells is understood to designate themacrophages, astrocytes, cytotoxic T lymphocytes (CTL) and killer (NK)cells as well as their derivatives such as, for example, LAKs (Versteeg1992 Immunology today 13: 244–247; Brittende et al 1996, Cancer 77:1226–1243). The expression “helper T lymphocytes” is understood todesignate in particular the CD4 cells which allow, after activation, thesecretion of factors for activating the effector cells of the immuneresponse. The polypeptides, and in particular the receptors expressed atthe surface of these cells and which are involved in the activation ofsuch cells, constitute in particular all or part of the TCR complex orCD3, all or part of the CD8, CD4, CD28, LFA-1, 4-1BB (Melero et al.,1998, Eur J Immunol 28: 1116–1121), CD47, CD2, CD1, CD9, CD45, CD30 andCD40 complexes, all or part of the cytokine receptors (Finke at al.,1998, Gene therapy 5: 31–39), such as IL-7, IL-4, IL-2, IL-15 or GM-CSF,all or part of the receptor complex for the NK cells such as for exampleNKAR, Nkp46, and the like; (Kawano et al., 1998 Immunology 95:5690–5693; Pessino et al., 1998 J Exp Med 188: 953–960), Nkp44, all orpart of the macrophage receptors such as for example the Fc receptor(Deo et al., 1997, Immunology Today 18: 127–135).

Numerous tools have been developed for introducing various heterologousgenes and/or vectors into cells, in particular mammalian cells. Thesetechniques may be divided into two categories: the first categoryinvolves physical techniques such as microinjection, electroporation orparticle bombardment. The second category is based on the use ofmolecular and cell biology techniques with which the gene is transferredwith a biological or synthetic vector which facilitates the introductionof the material into the cell in vivo. Nowadays, the most efficientvectors are the viral, in particular adenoviral and retroviral, vectors.These viruses possess natural properties for crossing the plasmamembranes, avoiding degradation of their genetic material andintroducing their genome into the nucleus of the cell. These viruseshave been widely studied and some are already experimentally used inhuman applications in vaccination, immunotherapy, or to compensate forgenetic deficiencies. However, this viral approach has limitations, inparticular due to the restricted cloning capacity in these viralgenomes, the risk of disseminating the viral particles produced in thebody and the environment, the risk of artefactual mutagenesis byinsertion into the host cell in the case of retroviruses, and thepossibility of inducing a high inflammatory immune response in vivoduring the treatment, which limits the number of injections possible(McCoy et al. 11995, Human Gene Therapy 6: 1553–1560; Yang et al., 1996Immunity 1: 433–422). Other alternative systems to these viral vectorsexist. The use of nonviral methods such as, for example, coprecipitationwith calcium phosphate, the use of receptors which mimic the viralsystems (for a summary see Cotten and Wagner 1993, Current Opinion inBiotechnology, 4: 705–710), or the use of polymers such aspolyamidoamines (Haensler and Szoka 1993, Bioconjugate Chem 4: 372–379).Other nonviral techniques are based on the use of liposomes whoseefficiency for the introduction of biological macromolecules such asDNA, RNA, proteins or active pharmaceutical substances has been widelydescribed in the scientific literature. In this domain, teams haveproposed the use of cationic lipids having a high affinity for the cellmembranes and/or nucleic acids. Indeed, it has been shown that a nucleicacid molecule itself could cross the plasma membrane of some cells invivo (WO 90/11092), the efficiency depending in particular on thepolyanionic nature of the nucleic acid. Since 1989 (Felgner et al.,Nature 337: 387–388), cationic lipids have been proposed to facilitatethe introduction of large anionic molecules, which neutralizes thenegative charges on these molecules and promotes their introduction intothe cells. Various teams have developed such cationic lipids: DOTMA(Felgner et al., 1987, PNAS 84: 7413–7417), DOGS or Transfectam™ (Behret al., 1989, PNAS 86: 6982–6986), DMRIE and DORIE (Felgner et al., 1993methods 5: 67–75), DC-CHOL (Gao and Huang 1991, BBRC 179: 280–285),DOTAP™ (McLachlan et al., 1995, Gene therapy 2: 674–622) orLipofectamine™, and the other molecules described in patents WO9116024,WO9514651, WO9405624. Other groups have developed cationic polymerswhich facilitate the transfer of macromolecules, in particular anionicmacromolecules, into cells. Patent WO95/24221 describes the use ofdendritic polymers, the document WO96/02655 describes the use ofpolyethyleneimine or polypropyleneimine and the documents U.S. Pat. No.5,595,897 and FR 2719316, the use of polylysine conjugates.

Given that it is desired to obtain in vivo a transformation targetedtoward a given cell type, it is evident that the vector used should beable to be “targeted” itself, as described above.

Use of cells transformed in vitro or ex vivo with vectors containing agene of therapeutic interest defined in relation to the proteins ofinterest identified in the present invention (SEQ ID No. 2, 4, 8, 9, 17,24) and the peptide sequences or the fragments of said sequencesbelonging to the same family of proteins chosen from Perlecan, theprecursor of the retinol-binding plasma protein, GM2 activator protein,calgranulin B and saposin B (for example SEQ ID No. 1, SEQ ID No. 3, SEQID No. 5 to 7, SEQ ID No. 10 to 16, SEQ ID No. 18 to 23, SEQ ID No. 25to 29) and the peptide sequences which exhibit at least 70% identity,preferably at least 80% identity and advantageously at least 98%identity with any one of the peptide sequences SEQ ID No. 1 to 29.

The present invention relates to a biological material for thepreparation of pharmaceutical compositions for preventing and treatingdegenerative and/or neurological and/or autoimmune diseases, preferablymultiple sclerosis, the composition comprising at least one cell, inparticular a cell not naturally producing antibodies, in a form allowingtheir administration into the body of a mammal, human or animal, as wellas optionally their prior culture, said cell being genetically modifiedin vitro by at least one nucleic acid sequence containing at least onegene encoding in vivo:

(i) at least one protein chosen from the proteins SEQ ID No. 2, 4, 8, 9,17, 24 and the peptide sequences or the fragments of said sequencesbelonging to the same family of proteins chosen from Perlecan, theprecursor of the retinol-binding plasma protein, GM2 activator protein,calgranulin B and saposin B (for example SEQ ID No. 1, SEQ ID No. 3, SEQID No. 5 to 7, SEQ ID No. 10 to 16, SEQ ID No. 18 to 23, SEQ ID No. 25to 29) and the peptide sequences which exhibit at least 70% identity,preferably at least 80% identity and advantageously at least 98%identity with any one of the peptide sequences SEQ ID No. 1 to 29 andthe peptide sequences which exhibit at least 70% identity, preferably atleast 80% identity and advantageously at least 98% identity with any oneof the peptide sequences SEQ ID No. 1 to 29, and any fragment,(ii) at least one peptide defined from the primary sequence of at leastone protein chosen from the proteins SEQ ID No. 2, 4, 8, 9, 17, 24 andthe peptide sequences or the fragments of said sequences belonging tothe same family of proteins chosen from Perlecan, the precursor of theretinol-binding plasma protein, GM2 activator protein, calgranulin B andsaposin B (for example SEQ ID No. 1, SEQ ID No. 3, SEQ ID No. 5 to 7,SEQ ID No. 10 to 16, SEQ ID No. 18 to 23, SEQ ID No. 25 to 29) and thepeptide sequences which exhibit at least 70% identity, preferably atleast 80% identity and advantageously at least 98% identity with any oneof the peptide sequences SEQ ID No. 1 to 29,(iii) at least any molecule inhibiting the function and/or bindingand/or expression of these proteins,(iv) at least one peptide derived from the primary sequence of a proteinchosen from the proteins SEQ ID No. 2, 4, 8, 9, 17, 24 and the peptidesequences or the fragments of said sequences belonging to the samefamily of proteins chosen from Perlecan, the precursor of theretinol-binding plasma protein, GM2 activator protein, calgranulin B andsaposin B (for example SEQ ID No. 1, SEQ ID No. 3, SEQ ID No. 5 to 7,SEQ ID No. 10 to 16, SEQ ID No. 18 to 23, SEQ ID No. 25 to 29) and thepeptide sequences which exhibit at least 70% identity, preferably atleast 80% identity and advantageously at least 98% identity with any oneof the peptide sequences SEQ ID No. 1 to 29, and capable of binding toat least one glycoprotein of the MHCI,(v) at least any antibody and any portion of antibody which are capableof binding to at least one protein chosen from the proteins SEQ ID No.2, 4, 8, 9, 17, 24, and the peptide sequences or the fragments of saidsequences belonging to the same family of proteins chosen from Perlecan,the precursor of the retinol-binding plasma protein, GM2 activatorprotein, calgranulin B and saposin B (for example SEQ ID No. 1, SEQ IDNo. 3, SEQ ID No. 5 to 7, SEQ ID No. 10 to 16, SEQ ID No. 18 to 23, SEQID No. 25 to 29) and the peptide sequences which exhibit at least 70%identity, preferably at least 80% identity and advantageously at least98% identity with any one of the peptide sequences SEQ ID No. 1 to 29.

More particularly, said target cell is obtained either from the mammalto be treated, or from a mammal other than that to be treated. In thelatter case, it should be noted that said target cell will haveundergone a treatment making it compatible with the mammal to betreated. The expression “mammal” is preferably understood to mean ahuman mammal. These cells are established as cell lines and arepreferably MHCII+ or MHCII+-inducible such as the lymphocytes,monocytes, astrocytes and oligodendrocytes.

The invention also relates to the modified cells and to a method forpreparing a cell as described above, characterized in that there isintroduced into a mammalian cell not naturally producing antibodies, byany appropriate means, at least one nucleic acid sequence containing atleast one gene of therapeutic interest and elements ensuring theexpression of said gene in said cell, said gene of therapeutic interestcontaining a nucleic acid sequence encoding a molecule or a moleculefragment in vivo, as described immediately above. More particularly, itrelates to prokaryotic cells, yeast cells and animal cells, inparticular mammalian cells transformed with at least one nucleotidesequence and/or one vector as described above.

According to a particular embodiment, the cells (dendritic cells,macrophages, astrocytes, CD4+ T lymphocytes, CD8+ T lymphocytes, and thelike) of the patient or allogenic cells are placed in contact with apurified preparation of the target polypeptide, the latter beinginternalized, made ready and presented at the cell surface associatedwith the MHCI and/or MHCII molecules and thus to induce a specificimmune response against the peptide. The “activated” cells are thenadministered to the patient in whom they will induce an immune responsespecific for the antigens (a natural route is used for the immuneresponse, but what the antigen-presenting cell is going to present ischecked).

According to a particular embodiment, the antigen-presenting cells(dendritic cell, macrophage, astrocytes, and the like) are modified invitro in order to express the antigens in the transformed cell whichwill associate with the MHCI and/or MHCII molecules and be presented atthe surface of the cells to induce a perfectly targeted immune reactionin the patient in whom the modified cell is administered.

All the vaccine approaches are not always satisfactory and lead, forexample, to limited immune reactions directed solely againstimmunodominant epitopes or against antigens exhibiting greatvariability. Likewise, the incorrect presentation of the antigens by theglycoproteins of the MHC system at the surface of the cells does notmake it possible to develop in the treated patient a suitableanti-protein of interest immunity. To overcome these problems, someauthors have proposed, in the context of such vaccine methods, to selectthe antigenic minimal fragments corresponding to the peptide portionscapable of being specifically recognized by the cytotoxic T lymphocytes,expressing them in the cells so that they associate with the moleculesof the MHCI and are presented at the surface of the cells in order toinduce a perfectly targeted immune reaction in the treated patient (Toeset al. 1997, PNAS 94: 14660–14665). More particularly, it has been shownthat epitopes of very small sizes (varying from 7 to about 13 aminoacids), which are expressed from minigenes introduced into a vacciniavirus, could induce a cellular type immunization. It has moreover beenshown that several minigenes could be conjointly expressed starting withthe same vector (this particular construct is called “string of beads”).Such a construct has the advantage of inducing a synergistic CTL-typeimmune reaction (Whitton et al., 1993 J. of Virology 67: 348–352).

Protocol for bringing the cells and the antigenic fragment into contact:

The presentation of the antigenic fragments by the MHCI moleculesdepends on an identified intracellular method (see Groettrup et al.,1996 Immunology Today 17: 429–435 for a review) in which very shortantigenic peptides (about 7–13 amino acids) are produced by degradationof a more complex polypeptide against which the final immune reactionwill be directed. These short peptides are then combined with the MHCIor MHCII molecules to form a protein complex which is transported to thecell surface in order to present said peptides to the circulatingcytotoxic T lymphocytes or to the circulating helper T lymphocytes,respectively. It should be noted, in addition, that the specificity ofthe MHCI or MHCII molecules toward the antigenic peptides varies as afunction of the MHCI or MHCII molecules (example for MHCI: HLA-A, HLA-B,and the like) and the allele (example for MHCI: HLA-A2, HLA-A3, HLA-A11)which are considered. Within the same animal species, from oneindividual to another, there is great variability of the genes encodingthe molecules of the MHC system (on this subject, see in particularGeorge et al., 1995, Immunology Today 16: 209–212).

According to a particular embodiment, the cells, such as dendriticcells, macrophages, astrocytes, CD4+ T lymphocytes, CD8+ T lymphocytes,are modified so as to express at their surface antibodies specific forthe targeted peptide. The peptide is neutralized with the antibodiesexpressed at the surface of the cells. These cells are preferably immunecells, preferably from the patient, are preferably cytotoxic andmodified to express all or part of an antibody specific for the targetpolypeptide.

Isolation of mononucleated cells from peripheral blood:

In 1968, Boyum described a rapid technique which makes it possible, bycentrifugation of blood on a density gradient, to separate themononucleated cells (lymphocytes and monocytes) with a good yield(theoretical yield 50%, that is to say 10⁶ cells/ml of blood). 50 ml ofperipheral blood sterilely collected in heparinized tubes arecentrifuged for 20 minutes at 150 g at 20° C. The cells recovered arediluted in two volumes of initial peripheral blood of sterile PBS. 10 mlof this suspension are deposited on 3 ml of a Ficoll-Hypaque solution(medium for separation of the lymphocytes, Flow). After centrifuging for20 minutes at 400 g and 20° C. without decelerating braking, themononucleated cells sediment at the PBS-Ficoll interface, as anopalescent dense layer, whereas practically all the red blood cells andthe polynuclear cells sediment at the bottom of the tube. Themono-nucleated cells are recovered and washed with sterile PBS.

Internalization of the antigens by the antigen-presenting cells:

Prior treatment of the antigen-presenting cells: the antigen-presentingcells are washed beforehand with PBS buffer containing 0.5% (w/v) BSA,then counted and they are then preincubated in the presence of variousreduction inhibitors three times in PBS-0.5% BSA containing 10 μM to 10mM final of DTNB (5,5′-dithio-bis-2-nitrobenzoic acid) or NEM(N-ethylmaleimide). The subsequent stages of binding of antigens to thecell surface or of internalization of antigens are also carried out inthe presence of various concentrations of inhibitors.

Protocol for internalization of the antigens by the antigen-presentingcells:

8×10⁶ cells are internalized in the presence of saturating quantity ofproteins radiolabeled with iodine 125 (1 μg) in microwells in 70 μl.After incubating for one hour at 4° C., with stirring, the antigens arebound to the surface of the cells. The cell suspension is washed twicein PBS-BSA and the cellular pellets are taken up in 70 μl of buffer andincubated at 37° C. for various periods ranging up to 2 hours. Cells andsupernatants are separated by centrifugation at 800 g for 5 minutes 4°C. For longer incubation periods, the preliminary stage of prebinding ofthe antigens to the surface of the cells is eliminated. The cells arediluted in RPMI-10% FCS medium in the presence of 20 mM Hepes, at 10⁶cells/ml. The cells are incubated in the presence of an excess ofantigen for various periods at 37° C. (1 μg of molecules/5×10⁷monocyte/macrophage cells or 10⁸ B-EBV cells).

All the therapeutic agents defined in the context of the presentinvention are used for preventing and/or treating a degenerative and/orneurological and/or autoimmune disease, such as multiple sclerosis,alone or in combination. They may also be used to evaluate theirefficacy in vitro or in vivo.

Administration of therapeutic agents in humans:

The biological material according to the invention may be administeredin vivo in particular in injectable form. It is also possible toenvisage injection by the epidermal, intravenous, intraarterial,intramuscular or intracerebral route with a syringe or any otherequivalent means. According to another embodiment, by oraladministration or any other means perfectly known to a person skilled inthe art and applicable to the present invention. The administration maytake place as a single dose or as a dose repeated once or several timesafter a certain time interval. The most appropriate route ofadministration and dosage vary as a function of various parameters suchas, for example, the individual or the disease to be treated, the stageand/or the progression of the disease, or alternatively the nucleic acidand/or protein and/or peptide and/or molecule and/or cell to betransferred or the target organ/tissue.

To carry out the treatment of the mammal mentioned in the presentinvention, it is possible to have pharmaceutical compositions comprisinga biological material as described above, advantageously combined with apharmaceutically acceptable vehicle for administration to humans or toanimals. The use of such carriers is described in the literature (see,for example, Remington's Pharmaceutical Sciences 16th ed. 1980, MackPublishing Co). This pharmaceutically acceptable vehicle is preferablyisotonic, hypotonic or exhibits low hypertonicity and has a relativelylow ionic strength, such as for example a sucrose solution. Moreover,said composition may contain solvents, aqueous or partially aqueousvehicles such as sterile water, free of pyrogenic agents and dispersionmedia for example. The pH of these pharmaceutical compositions issuitably adjusted and buffered according to conventional techniques.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 represents the amino acid sequence of the GM2AP protein (SEQ IDNO: 73), and the localization of the peptides, which is underlined, andwhich are used for the production of anti-GM2AP peptides antibodies.

FIG. 2 represents the amino acid sequence of the MRP14 protein (SEQ IDNO: 75), and the localization of the peptides, which is underlined, andwhich are used for the production of anti-MRP14 peptides antibodies.

FIG. 3 represents the amino acid sequence of the Saposin B protein (SEQID NO: 74), and the localization of the peptides, which is underlined,and which are used for the production of anti-Saposin B peptidesantibodies.

FIG. 4 represents the assay of the MRP8 protein (ng/ml—on the y-axis) inthe urine of patients suffering from multiple sclerosis (MS), in theurine of patients suffering from other neurological diseases (OND) andin the urine of controls considered healthy (HC). n means the number ofurine samples tested per category.

FIG. 5 represents the assay of the MRP14 protein (ng/ml—on the y-axis)in the urine of patients suffering from multiple sclerosis (MS), in theurine of patients suffering from other neurological diseases (OND) andin the urine of controls considered healthy (HC). n means the number ofurine samples tested per category.

FIG. 6 represents the assay of the MRP8/14 protein (ng/ml—on the y-axis)in the urine of patients suffering from multiple sclerosis (MS), in theurine of patients suffering from other neurological diseases (OND) andin the urine of controls considered healthy (HC). n means the number ofurine samples tested per category.

FIG. 7 represents the mean concentrations of the MRP8, MRP14 and MRP8/14proteins (ng/ml—on the y-axis) in the urine of patients suffering frommultiple sclerosis (MS), in the urine of patients suffering from otherneurological diseases (OND) and in the urine of controls consideredhealthy (HC). n means the number of urine samples tested per category.

FIG. 8 represents the assay of the GM2AP protein (ng/ml—on the y-axis)in the urine of patients suffering from multiple sclerosis (MS), in theurine of patients suffering from other neurological diseases (OND) andin the urine of controls considered healthy (HC). n means the number ofurine samples tested per category. MS means multiple sclerosis, ONDmeans other neurological diseases and Healthy means samples fromcontrols supposed healthy (HC).

FIG. 9 represents the assay of the Saposin B protein (μg/ml—on they-axis) in the urine of patients suffering from multiple sclerosis (MS),in the urine of patients suffering from other neurological diseases(OND) and in the urine of controls considered healthy (HC). n means thenumber of urine samples tested per category. MS means multiplesclerosis, OND means other neurological diseases and Healthy meanssamples from controls supposed healthy (HC).

FIG. 10 represents the codetection of the Saposin B (μg/ml—on they-axis) and GM2AP (ng/ml—on the x-axis) proteins in urine samples fromMS patients, controls supposed healthy and patients suffering from otherneurological diseases and the correlation observed between the levels ofthe two proteins.

FIG. 11 represents: FIG. 11A, the assay of the GM2AP protein in ng/ml inthe urine of an MS patient in progressive remittent form (light-coloredcurve) and the gliotoxicity as a percentage of dead cells estimated bythe MTT test (dark-colored curve); FIG. 11B, the assay of the Saposin Bprotein in μg/ml in the urine of an MS patient in progressive remittentform (light-colored curve) and the gliotoxicity as a percentage of deadcells estimated by the MTT test (dark-colored curve).

FIG. 12 represents the product of the concentrations of the GM2AP andsaposin B proteins in ng×μμg/ml² in the urine of an MS patient inprogressive remittent form (light-colored curve) and the gliotoxicity asa percentage of dead cells estimated by the MTT test (dark-coloredcurve).

FIG. 13 represents: FIG. 13A, the assay of the GM2AP protein in ng/ml inthe urine of an MS patient in progressive remittent form (light-coloredcurve) and the gliotoxicity as a percentage of dead cells estimated bythe MTT test (dark-colored curve); FIG. 13B, the assay of the Saposin Bprotein in μg/ml in the urine of an MS patient in progressive form(light-colored curve) and the gliotoxicity as a percentage of dead cellsestimated by the MTT test (dark-colored curve).

FIG. 14 represents the product of the concentrations of the GM2AP andsaposin B proteins in ng×μg/ml² in the urine of an MS patient inprogressive form (light-colored curve) and the gliotoxicity as apercentage of dead cells estimated by the MTT test (dark-colored curve).

FIG. 15 represents the correlation between the concentrations of GM2APin ng/ml α-axis) and gliotoxicity as a percentage of dead cellsestimated by the MTT test (y-axis) determined in the urine of MSpatients and of controls.

FIG. 16 represents the correlation between the concentrations of SaposinB in μg/ml (x-axis) and gliotoxicity as a percentage of dead cellsestimated by the MTT test (y-axis) determined in the urine of MSpatients and of controls.

FIG. 17 represents the correlation between the product of theconcentrations of GM2AP and Saposin B in ng×μg/ml² (x-axis) andgliotoxicity as a percentage of dead cells estimated by the MTT test(y-axis) determined in the urine of MS patients and of controls.

FIG. 18 represents the correlation between the concentrations of GM2AP(ng/ml—on the left-hand y-axis), the concentrations of Saposin B(μg/ml—right-hand y-axis) and the gliotoxicity as a percentage of deadcells estimated by the MTT test (x-axis). Two estimated correlationstraight lines are represented on the graph. The lines in bold relate tothe concentrations of saposin B; the lines in light black relate to theconcentrations of GM2AP.

DETAILED DESCRIPTION OF EMBODIMENTS EXAMPLES Example 1 Collecting andPooling of Urines

Urine samples of different volumes were collected from healthyindividuals (MS-negative) having a priori no neurological or autoimmunedisease. The toxic activity of each sample toward murine astrocyte cellswas tested in vitro using the MTT test. In total, a pool of 20 liters ofurine was formed (MS-negative pool). In parallel, urine samples ofdifferent volumes were collected from individuals suffering frommultiple sclerosis (MS-positive) at various stages of the disease. Thetoxic activity of each sample toward murine astrocyte cells was testedin vitro using the MTT test. In total, a pool of 80 liters of urine wasformed (MS-positive pool).

Example 2 Purification of the Urinary Proteins

The pools of MS-positive and MS-negative urine, collected and testedaccording to example 1, were purified in order to obtain a high proteinconcentration and to remove the high molecular weight proteins as far aspossible.

Precipitation: precipitations with ammonium sulfate (Prolabo—ref. 21 333365) were carried out on the pools of MS-positive and MS-negative urine.The percentage of 60% saturated ammonium sulfate per 40% of urine, thatis 390 grams of ammonium sulfate per liter of urine, was used. Each poolwas distributed into fractions of 1.8 liters in 2-liter bottles in orderto improve the precipitation. The precipitation was carried out for 2×8hours, at room temperature, with gentle stirring. After centrifugationof the pools of urine at 3 000 rpm for 10 min, at a temperature of 10°C., the pellet obtained is taken up in 20 mM Tris buffer containing 1 mMCaCl₂ and 0.25 M urea. The mixture was then centrifuged at 3 000 rpm for10 min. The supernatant contains the concentrated proteins. It is eitherused immediately for the next stage, or frozen if the next stage cannotbe performed continuously.

Ion-exchange chromatography: the solution containing the proteins wasthen passed over a DEAE fast Flow gel (marketed by PHARMACIA). Thisstage is carried out at low pressure on a PHARMACIA column filled withgel. The buffers are brought to the column by a peristaltic pump whichallows a uniform flow rate. The buffer for equilibrating the column is20 mM Tris buffer, pH 7. The fraction corresponding to the precipitationsupernatant and containing an excessively high quantity of salts isdialyzed against this buffer before depositing on the column. Elutionwith a salt gradient makes it possible to recover the proteins. Theelution gradient is performed in steps of 100, 200, 300, 500 mM NaCl inthe buffer for equilibrating the column. The elution fractions aretested by the MTT test and only the positive fractions, that is thefraction eluted at 200 Mm NaCl, will be preserved. These fractions maybe immediately treated or stored in the freeze-dried state.

Purification: steric exclusion chromatography based on the difference insize and shape of the proteins to be eluted was used. The fractioncorresponding to the 200 mM NaCl elution is deposited on the column.During the elution, the proteins of low molecular mass are retained andtherefore eluted later than the large molecules. The purifications werecarried out on HPLC with a TosoHaas TSK Prep G 3000 SW column having adiameter of 21.5 mm and a length of 300 mm, the molecular mass exclusionlimit is 500 000 daltons. The elution buffer used contains 100 mMphosphate, 100 mM sodium sulfate, at pH 6.8. The separation of theprotein mixture was carried out in 60 min. Only the fractioncorresponding to a mass of 15–20 000 daltons was preserved. Thisfraction is dialyzed in 20 mM Tris buffer containing 0.2 mM CaCl₂, pH7.2, and then freeze-dried.

At each stage, only the fractions having a significant toxic activitywere retained for the next stage. The toxic activity of the proteins waschecked at each stage using the MTT test. Only the fractions having asignificant toxic activity were retained for the additional purificationstage described in example 3.

Example 3 Additional Purification of the Urinary Proteins by ReversePhase Chromatography

Pools of urine from MS patients (MS-positive pool) and from non-MSpatients (MS-negative pool), obtained after purification according toexample 2, were taken up in distilled water and then diluted with a 0.2%TFA/10% acetonitrile solution in order to obtain a final concentrationof about 130 to 140 μg/ml.

The separation by C8 reverse phase HPLC was carried out on a BrownleeAquapore column (trade name) marketed by the company Perkin Elmer(column characteristics: 300 angstroms/7 μm/(100×4.6) mm). Two separatecolumns were used for the positive and negative pools respectively. Theinjections were carried out by multiple injections of 250 μl. Theproteins were eluted with a linear gradient from 5% to 15% of buffer Bover 5 min, and then from 15% to 100% of buffer B over 95 min, at a flowrate of 0.5 ml/min. The separation buffers A and B used are the buffer0.1% TFA (Pierce No. 28904)/MilliQ water and the buffer 0.09% TFA/80%acetonitrile (Baker) respectively. The detection was carried out bymeasuring the UV absorbence at 205 and 280 nm. Fractions were collectedin 1.5 ml and 0.5–1 ml fractions in the zone of interest. The fractionswere frozen after collection in dry ice.

The fractions collected were then dried in a speed vac and taken up in100 μl of 0.1% TFA/30% acetonitrile, 20 μl of the fractions weretransferred into 500 μl eppendorfs, dried and washed twice with 100 μlof MilliQ water and then dried again.

The toxic activity of the proteins contained in each fraction collectedafter elution was determined with the aid of the MTT test. Only fraction21 exhibiting a significant toxic activity was retained. The number forthis fraction corresponds to the order of elution as a function of theelution conditions stated in this example.

Example 4 Analysis of the Proteins Obtained by HPLC Separation onSDS-TRICINE Gel

The collection pool for fraction 21 obtained by HPLC, as described inexample 3, and resulting from 20 injections of the MS-positive pool, wasdeposited on a precast 16% SDS-TRICINE gel of 10 wells and 1 mm thick(marketed by the company Novex). The conditions for using the gelcorrespond to those recommended by the supplier. The sample is taken upin 75 μl of 1 times concentrated sample buffer (SDS-TRICINE No. LC 1676,1 ml two times concentrated+50 μl of β-mercapto-ethanol (Pierce) diluted½ in water) and 25 μl of the sample are deposited on the gel in threeportions. The collection pool for fraction 21 obtained from 6 injectionsof the MS-negative pool was deposited on the gel under the sameconditions as described for the MS-positive pool. The migration on thetwo gels was carried out in parallel in the same migration tank (XCELLII NOVEX (trade name)) at a constant voltage of 125 mV for 2 hours. Thetank is placed in a container containing ice. The gels were staineddirectly after migration by zinc/imidazole staining (staining kit161-0440 marketed by the company BIORAD) so as to obtain a reversiblenegative staining. The protein bands are translucent on an opaque base.

Example 5 Digestion of the Gel Bands with Trypsin

All the protein bands visualized in the deposits of fraction 21 were cutout and subjected to proteolysis with trypsin.

The gel bands are cut out with a scalpel into slices of 1 mm andtransferred into eppendorf tubes. The eppendorfs are subjected to acentrifugation peak so as to cause the gel pieces to fall and, aftercentrifugation, 100 μl of washing buffer (100 Mm NH₄CO₃/50% CH₃CN) areadded to the gel pieces. After stirring for 30 min at room temperature,the supernatant is removed in fractions of 20 μl and the washing step isrepeated twice. The eppendorfs are dried for 5 min in speed vac. 20 μgof trypsin (modified sequenal grade PROMEGA V5111) are taken up in 200μl of digestion buffer (5 mM TRIS, pH 8) and are dissolved for 30 min atroom temperature, with intermittent stirring, and 20 to 30 μl ofresuspended trypsin are added to the gel pieces. The eppendorfs arecentrifuged and stored in a hot room at 28° C. overnight. Afterdigestion, the gel bands may be used immediately for the measurements ofmass or frozen for subsequent use.

Example 6 Chemical Digestion of the Gel Bands with CNBR

In the event of a protein being resistant to enzymatic cleavages, inparticular to the action of trypsin as described in example 5, the bandsbetween 16 kD and 20 kD were treated with CNBR. The gel bands, alreadyused for the digestions with trypsin, are dried for 5 to 10 min in speedvac.

A solution of CNBR (FLUKA) at 200 mg/ml was prepared in 70% formic acid(BAKER). 20 μl of this solution were used to rehydrate the gel pieces.The reaction was carried out for 20 h at room temperature and in thedark. The peptides are extracted for 3 times 30 min with 100 μl of 0.1%TFA/60% acetonitrile. The extraction solutions are combined andconcentrated to 20 μl. These samples are diluted 5-fold in 0.1%TFA/water. The separation conditions are those described for thepeptides from the digestion with trypsin.

Example 7 Analysis by MALDI-TOF Spectrometry

30 μl of extraction buffer (2% TFA/50% acetonitrile) are added to thesamples. The eppendorfs to be analyzed are subjected to a centrifugationof 5 min, and then to a sonication of 5 min, and finally to acentrifugation of 1 min.

On a stainless steel disk, 14 deposits of 0.5 μl of matrix(α-cyano-4-hydroxytranscinnamic acid at saturation in acetone) arecarried out. A fine uniform microcrystalline layer is obtained. 0.5 μlof a solution of 2% TFA/water are deposited on this sublayer on the 14deposits, and then 0.5 μl of sample to be analyzed are added. 0.5 μl ofa solution at saturation with α-cyano-4-hydroxytranscinnamic acid acidin 50% acetonitrile/water is added to this drop thus formed. Afterdrying at room temperature for 30 min, the crystalline deposits arewashed with 2 μl of water which are immediately evacuated by a puff ofair. All the spectra are obtained on a BRUKER BIFLEX (trade mark) massspectrometer equipped with a reflectron. The measurements (90 to 120laser shots on the entire deposit) are accumulated in order to obtain amass spectrum which is most representative of all the peptides presentin the matrix-sample sandwich. For each deposit, a calibration with thepeptides from the autolysis of trypsin was made in order to be able touse a measurement accuracy of less than 100 ppm.

Searches in databanks were carried out in MS-FIT PROTEINPROSPECTOR(http://prospector.ucsf.edu). The common parameters used in thesesearches are (1) database: NCBInr, (2) a tolerance of 100–50 ppm, (3)the cysteins are not modified, (4) the methionines may be oxidized, (5)molecular weight range: 1 000–100 000 Da, (6) up to 3 cleavage sites maybe ignored.

Example 8 N-Terminal Sequencing of the Digestion Peptides

(i) Extraction and Separation by HPLC of the Digestion Peptides.

After the measurements of mass on the entire digestion, the rest of thepeptides are extracted 3 times 30 min in a sonication bath with 0.1%TFA/60% acetonitrile. The extraction solutions are combined and dried upto 20 μl in speed vac. After dilution in 80 μl of buffer A (0.1%TFA/water), the extractions of the gel bands, digested with trypsin, areinjected onto a C18/MZ-Vydac/(125×1.6) mm/5 μm column. The elution ofthe peptides is carried out at a flow rate of 150 μl/min, in a gradientranging from 5% of buffer B (0.09% TFA/80% acetonitrile) to 40% ofbuffer B over 40 min, and then from 40% of buffer B to 100% of buffer Bover 10 min. The detection is made by measuring the UV absorbence at 205nm. The collection of the peaks is carried out in 500 μl eppendorftubes. The fractions are stored on ice and, for the band of 18–20 kD ofthe MS-positive pool 21, analyzed by MALDI-TOF mass spectrometry.

(ii) N-Terminal Sequencing

The fractions corresponding only to a single mass peak were analyzed byEdman degradation on a sequencer (model 477A PERKIN ELMER/AppliedBiosystems). The sequencing conditions are those described by themanufacturer. A microcartridge was used for depositing the samples andthe PTH-amino acids are identified with an online HPLC system (model120A PERKIN ELMER/Applied Biosystems).

The deposition of the fraction to be sequenced is made in severaldepositions of 15 μl with intermediate dryings. The tube which containedthe peptide is washed with 15 μl of 85% formic acid (BAKER). The aminoacid sequences still correspond to the masses measured. The peptides,whose masses do not correspond to the principal protein identified, weresequenced as a priority. In this manner, it was possible to identify upto three proteins in a gel band.

Example 9 Results and Discussion

After reversed HPLC of the MS-negative control pool and of theMS-positive pool, the toxic activity of each elution fraction wasdetermined using the MTT test. Only fraction 21 of the MS-positive poolexhibits a toxic activity in vitro. Fraction 21 of the MS-negativecontrol pool exhibits no toxic activity. The toxic activity of fraction21 of the MS-positive pool was confirmed in vitro by FACS, as describedin patent application WO 98/11439 on murine astrocyte cells.

The protein content of fraction 21 of the MS-negative control pool andof the MS-positive pool was observed after separation on 16% SDS-TRICINEgel and staining of the gel with zinc/imidazole. Proteins of highapparent molecular weights were found in the two fractions. On the otherhand, five different bands of low apparent molecular weights are onlyvisible in fraction 21 of the MS-positive pool (bands 8, 14, 18 and 20kD). To each band there corresponds at least one protein and variants ofsaid proteins which have an apparent molecular weight close to that ofthe native protein. These variant sequences exhibit a percentagehomology or identity with the native sequences of at least 70%,preferably of at least 80% and advantageously of at least 98%.

The proteins of interest of fraction 21 of the MS-positive pool werethen analyzed by mass spectrometry and/or sequencing and searching forhomology in the databanks. The results show the presence of five proteinbands migrating between 22 and 5 kD in fraction 21 of the MS-positivepool and variants of said proteins.

These proteins are the C-terminal fragment of Perlecan, which starts atamino acid 3464 and ends at amino acid 3707 of the complete proteinsequence, identified in the sequence identifier SEQ ID No. 2, theprecursor of the retinol-binding plasma protein whose sequence is givenin SEQ ID No. 4, the GM2 activator protein identified in SEQ ID No. 8,calgranulin B identified in SEQ ID No. 17 and saposin B represented inSEQ ID No. 24. As described above, homologs or variants of said proteinswere also identified by sequencing. These homologous or variant proteinsequences are the product of mutations in the genes encoding saidproteins. By way of example, SEQ ID No. 9 exhibits 99% homology oridentity with SEQ ID No. 8 of the GM2 activator protein and the fragmentof SEQ ID No. 9 which starts at amino acid 34 and ends at amino acid 202exhibits 98.88% homology or identity with the fragment corresponding tothe native protein identified in SEQ ID No. 8.

Example 10 Identification of the Proteins in a Urine Sample

Urine samples from an MS-negative individual and from an MS-positivepatient were collected. These urine samples were purified according tothe protocol described above. The final elution fractions 21 wereanalyzed separately by mass spectrometry. The mass profile of eachfraction corresponding to each urine sample was compared with the massprofile obtained for the proteins identified in the preceding examples.The results show that for the urine sample from the MS-positive patient,the masses correspond to the molecules (i) C-terminal fragment ofPerlecan, (ii) GM2 activator protein, (iii) calgranulin B and (iv)saposin B identified above. On the other hand, none of these masses wasidentified in the mass profile obtained after analysis of the urinesample obtained from the MS-negative individual. The method describedcan be used as a diagnostic assay.

Example 11 Western Blot Assay

Western blottings were carried out on different fractions of crude orpurified urine as described in example 2. Urine samples from healthyindividuals and from patients suffering from multiple sclerosis aretested in parallel. The samples are deposited on an electrophoresis gelwhich makes it possible to separate the various proteins according totheir molecular mass under the action of an electric field. The Westernblottings are carried out after transferring the proteins from the gelonto a membrane. To visualize the transferred proteins, the membrane issaturated with saturation buffer and then incubated with an antibodydirectly labeled with alkaline phosphatase. The antibody used is ananticalgranulin antibody (mouse monoclonal antibody, clone CF 145subtype IgG 2b marketed by the company Valbiotech: reference MAS 696pbatch PC96G696). The substrate for the enzyme is3,3′-(1,1′-biphenyl)-4,4′-diazonium dichloride and sodium2-naphthalenylphosphate (marketed under the name β Naphthyl acidphosphate Sigma ref. N7375 and Tetrazotized ô-dianisine D3502) is addedfor revealing the bands and visualizing the proteins linked to theantibody. A molecule with an apparent molecular mass of about 14 000 isrevealed in the purified urines from patients suffering from MS, with arelatively intense signal. This protein corresponds to calgranulin B(apparent molecular mass: 14 kD). By contrast, no signal is observedfrom urine from healthy individuals. This observation confirms thepresence of this protein specifically in the urines from patientssuffering from MS and the use of a method of detection using an antibodyrecognizing the protein.

Example 12 Production of Monoclonal Antibodies

The production of monoclonal antibodies using ascites requirescompatibility of the H-2 system between the hybridoma and the producingmouse. Twenty 6-week-old female Balb/c mice receive an injection of 0.5ml of Pristane (2,6,10,14-tetramethylpentadecane acid) in theirperitoneal cavity, for the production of ascites (Porter et al., 1972).One week to 10 days later, 5×10⁶ to 10×10⁶ hybridomas, diluted in 0.5 mlof sterile buffer containing 0.145 M NaCl, 10 mM Na₂HPO₄, 2.7 mM KCl and1.5 mM KH₂PO₄ at pH 7.4, are injected by the intraperitoneal route. Theascites appear one to two weeks later. The ascitic fluids present in theperitoneal cavity are then collected with a syringe after incision ofthe peritoneum. The fluid collected is centrifuged at 3 000 g for 15minutes at room temperature, filtered on gauze in order to remove thefat, and then buffered by adding 1/20th of its volume of 1M Tris-HCl atpH 8.0. This method makes it possible to obtain quantities of antibody10 times higher than those obtained by hybridoma culture.

The immunoglobulins present in the ascitic fluid are released by thesalts (ammonium sulfate or sodium sulfate). The ascitic fluid isprecipitated with 40% ammonium sulfate. After 20 minutes in the cold,the solution is centrifuged for 15 minutes at 8 000 g at 4° C. Theprecipitate is washed and resuspended in the cold in a 40% ammoniumsulfate solution and then centrifuged again. The new precipitateenriched with IgG is redissolved in PBS buffer and dialyzed overnightagainst the 25 mM Tris-HCl buffer containing 150 mM NaCl, pH 7.4. Inparallel, an agarose-Protein A (or protein G) column (marketed in thefreeze-dried form, Pierce) is extensively washed with the 25 mM Tris-HClbuffer containing 150 mM NaCl, pH 7.4. The solution enriched with IgG isdeposited on the column and then the column is washed. The IgGs retainedby the column are eluted at acidic pH (200 mM glycine, pH 2.8). Theeluted fractions are neutralized with one volume of 1M Tris-Base, pH10.5. The immunoglobulin content of each fraction collected isquantified by reading the absorbance at 280 nm (e 1%, 1 cm=14.0, Prahland Porter 1968). The rich fractions are pooled. The degree ofpurification of the pooled IgGs is analyzed by acrylamide gelelectrophoresis in the presence of SDS. The purified IgGs are dialyzedovernight against the 25 mM Tris-HCl buffer containing 150 mM NaCl, pH7.4, sterilely filtered, aliquoted and stored at −20° C. Their finalconcentration is determined by reading the absorbance at 280 nm or bymicro-BCA assay. The immunogenic peptides designated by the referencesSEQ ID No. 58, SEQ ID No. 54, SEQ ID No. 55, SEQ ID No. 56, SEQ ID No.57, SEQ ID No. 58, SEQ ID No. 59, and SEQ ID No. 65 were used for theproduction of monoclonal antibodies, according to the protocol describedabove. However, it is in the capability of persons skilled in the art todefine other protocols for the production of monoclonal antibodies, forexample using the techniques described by Köhler and Milstein and byGalfre G. et al. previously cited or techniques derived therefrom.

Production of recombinant proteins and of polyclonal and monoclonalantibodies

Recombinant proteins:

The recombinant proteins GM2AP (SEQ ID NO. 73) and Saposin B (SEQ ID NO.74) used to produce the calibration series for this study were producedin a prokaryotic system and purified from the clones of these twoproteins obtained in our laboratory using the methods and protocols wellknown to persons skilled in the art.

Anti-GM2AP or Anti-Saposin B Antibodies:

The anti-GM2AP or anti-Saposin B antibodies used to carry out the studywere produced in our laboratory or generously given.

Anti-Saposin B and anti-GM2AP polyclonal antibodies (Li et al.,Glycoconjugate, 1984) were used for the study (cf the examples below):they are called SAP84 and GM2AP84.

Anti-GM2AP or anti-Saposin B polyclonal antibodies were produced andpurified in the laboratory using the protocols and methods well known topersons skilled in the art: 50 μg of prokaryotic GM2AP or Saposin Bprotein purchased were injected into rabbits on days D0, D28 and D56;two booster injections were carried out once per month for twoconsecutive months. The two anti-GM2AP polyclonal antibodies and twoanti-Saposin B polyclonal antibodies were thus obtained and theirspecificity toward the recombinant protein was verified by Westernblotting and Elisa.

Anti-GM2AP or Saposin B peptides polyclonal antibodies were produced andpurified in the laboratory using the protocols and methods well known topersons skilled in the art: 75 μg of GM2AP or Saposin B peptidesdefined, produced and coupled to KLH in our laboratory were injected ondays D0, D28 and D56; several boosts were thus carried out once permonth for 5 consecutive months with injection of 75 μg each time. Fouranti-GM2AP peptides polyclonal antibodies, four anti-Saposin B peptidespolyclonal antibodies and four anti-MRP14 peptides rabbit polyclonalantibodies were obtained and their specificity toward the recombinantprotein was verified by Western blotting and by Elisa. The sequence ofthe GM2AP, Saposin B and MRP14 peptides chosen are described in FIGS. 1to 3.

The following were obtained:

an antibody anti-mixture of two peptides of 13 and 15 amino acids ofGM2AP: 189–190; an antibody anti-peptide of 18 amino acids of GM2AP:191–192 (cf. FIG. 1),

an antibody anti-mixture of two peptides of 13 and 19 amino acids ofMRP14: 193; an antibody anti-peptide of 17 amino acids of MRP14: 195–196(cf. FIG. 2),

an antibody anti-mixture of three peptides of 12, 15 and 15 amino acidsof Saposin B: 74–75; another antibody anti-mixture of 3 peptides of 12,15 and 15 amino acids of Saposin B: 72–73 (cf. FIG. 3).

Anti-native fraction monoclonal antibodies were produced and purified inthe laboratory using the protocols and methods well known to personsskilled in the art. The “native fraction” corresponds to the cytotoxicelution fraction obtained from the pool of 80 liters of urine from MSpatients and after purification. It is the last elution fraction whichcontains the three proteins GM2AP, Saposin B, MRP14. 30 μg of thispurification fraction were injected into three mice on days D0, D14, D28and the sample collection was carried out on D38. After “screening” andcell fusion, protocols known to persons skilled in the art forestablishing hybridomas and monoclonal antibodies, the hybridomas werereinjected into the mice and the ascitic fluid was recovered 10 dayslater. The antibodies were purified on sepharose-Protein A column andthe specificity toward the fraction used for the immunization wasverified by Western blotting and by Elisa. Thus, four monoclonalantibodies were obtained: 191C1A7, 3D3F9, 18C8C5 and 7D12A8.

Example 13 Assay of the MRP14 Proteins in the Urines by the ELISATechnique

The MRP14, MRP8 proteins and the MRP8/14 heterocomplex were assayed inhuman urines using (i) either an Elisa assay technique according to themethod known to persons skilled in the art and using the anti-MRPantibodies described in the preceding examples; (ii) or the “MRP EnzymeImmunoassay” kit marketed by BMA Biomedicals AG, Augst, Switzerland,using the antibodies of the kit, the protocol being carried outaccording to the leaflet in the kit.

Detection of MRP14 and MRP8/14 in Urines

The assay was carried out using 17 urines of individuals from the activepopulation (HC), 27 urines of patients suffering from multiple sclerosis(MS) and 7 urines of patients suffering from other neurological diseases(OND).

FIG. 4 illustrates the levels of MRP8 assayed in these urines: while theMRP8 concentration is practically zero in the OND urines, there is noreal difference in distribution between the HC and MS urines. It shouldbe noted, however, that the differences observed are practicallynegligible because the concentrations assayed are extremely low.

FIG. 5 illustrates the levels of MRP14 assayed in the same urines: whilethere are no real differences in the distribution of the concentrationsbetween the HC and OND urines, the concentrations are higher in certainMS urines.

FIG. 6 illustrates the levels of MRP8/14 hetero-dimer assayed in thesame urines: while there is no real difference between theconcentrations of the HC and OND urines, higher concentrations areobserved in certain MS urines, perhaps corresponding to a subpopulationof MS patients characterized by an activity of the disease. MRRP8/14assayed in the urines is a marker for the activity of the MS diseasecharacterized by an inflammation peak).

The recapitulative FIG. 7 confirms that there is no significantdifference in MRP8 and MRP14 concentration between the HC, OND and MSurines, while a small difference in MRP8/14 concentration is observedbetween these urines, this concentration being higher on average in theMS urines and being a marker for the activity of the disease(inflammation peak).

Example 14 ELISA Protocols Used for the Assay of the GM2AP and Saposin BProteins

The GM2AP or Saposin B proteins were assayed in human urines usinganti-GM2AP or anti-Saposin B? polyclonal antibodies according to theElisa protocol described by Gardas et al. (Glycoconjugate Journal 1,37–42, 1984). The principal stages are briefly described below:

At each stage, the wells of a 96-well microplate are filled with 200 μlof the designated solution. The wells are first “coated” with a solutionof GM2AP (prokaryotic recombinant protein) diluted to 50 ng/ml in acarbonate-bicarbonate buffer, pH 9.6. After incubating overnight at 4°C., the solution is removed and the wells are washed four times with PBSbuffer pH 7.4 containing 0.05% Tween-20 (PBS-Tween). The microplatesthus coated are stored at 4° C. for about 2 weeks.

The urine samples at three different dilutions (20×, 40× and 80× orother appropriate dilutions) are incubated with an appropriate dilutionof the anti-GM2AP or anti-Saposin B rabbit polyclonal antibody overnightat 4° C. A standard series of dilutions of a recombinant protein rangingfrom 2.0 to 62.5 ng/ml is used to prepare the calibration series and aretreated in the same manner. All the dilutions are made in PBS-Tweenbuffer containing 1 mg/ml of ovalbumin. Thus, 0.2 ml of each incubatedsolution is added to “coated” wells in duplicate and the plates are leftfor 2 hours at room temperature. The wells are then washed four times inPBS-Tween and again filled with a solution of anti-rabbit IgG goatantibodies coupled to peroxidase and diluted about 1 200-fold. Afterincubating for 2 hours at room temperature, the wells are washed fourtimes in PBS-Tween and again filled with the staining reagent. Thestaining reagent consists of 100 mg of2,2′-azino-di-(3-ethylbenzothiazoline)sulfonic acid and 10 μl of 30%hydrogen peroxide for one hour at room temperature and the degree ofstaining of each microwell is estimated by reading the absorbance at 405nm.

A standard curve is constructed by placing on the x-axis theconcentration of GM2AP in the calibration series or of Saposin B with alogarithmic scale and on the y-axis the percentage absorbance with alinear scale. The percentage absorbance of the sample is the absorbanceratio between the urine sample and the control which contains only theantiserum, without the soluble antigen.

A solution of recombinant protein GM2AP produced in a prokaryoticsystem, and having a concentration of 3 mg/ml, is diluted in 50 mMcarbonate buffer, pH 9.6, and 50 μl are added to each well of a 96-wellmicroplate, that is 50 μl per well of a solution at 0.5 μg/ml. Theplates thus prepared are incubated overnight at room temperature. Theanti-GM2AP polyclonal antibody produced in the laboratory (rabbit 79)was purified and diluted in PBS-0.05% Tween buffer in the presence of10% horse serum. This solution is diluted 1/8 000. The solution is usedto produce a calibration series with 8 series points coveringconcentrations from 0 to 500 ng/ml. A preincubation is carried outovernight at room temperature between 100 μl of antibody and 100 μl ofurine sample to be assayed or of recombinant GM2AP or Saposin B proteinsolution serving for the calibration series. After washing themicroplate in PBS-Tween, 50 μl of the incubation mixture are added perwell, and then incubated for two hours at room temperature. Themicroplate is again washed in PBS-Tween, and then 50 μl of anti-rabbitIgG antibody coupled to peroxidase and diluted 1/5 000 are added to eachmicrowell of the plate and incubated for two hours at room temperature.After further washings of the microplate, 100 μl of OPD are added toeach well and incubated for 20 minutes at room temperature. The stainingof each well, proportional to the concentration of GM2AP or of Saposin Brecognized by the specific antibody used, is estimated by reading theabsorbance.

A solution of recombinant protein GM2AP or Saposin B produced in aprokaryotic system, with a concentration of 3 mg/ml, is diluted in 50 mMcarbonate buffer, pH 9.6, and 50 μl are added to each well of a 96-wellmicroplate, that is 50 μl per well of a solution at 1.5 μg/ml. Theplates thus prepared are incubated overnight at room temperature. Thepurified anti-GM2AP peptides polyclonal antibodies produced in thelaboratory (rabbit 190 and rabbit 191) are used alone or as a mixture,diluted 1/1 000 for each, in PBS-0.05% Tween buffer in the presence of10% horse serum. The calibration series is produced using theprokaryotic recombinant protein GM2AP or Saposin B diluted so as tocover the concentration range 0 to 1 500 ng/ml with 8 points. 100 μl ofantibody (one antibody or the two together) are preincubated in thepresence of 100 μl of urine sample to be tested or of recombinant GM2APor Saposin B solution, overnight at room temperature. After washing themicroplate in PBS-Tween, 50 μl of the incubation mixture are added perwell and then incubated for two hours at room temperature. Themicroplate is again washed in PBS-Tween, and then 50 μl of anti-rabbitIgG antibody coupled to peroxidase, diluted 1/5 000, are added to eachmicrowell of the plate and incubated for two hours at room temperature.After washing the microplate, 100 μl of OPD are added to each well andincubated for 20 minutes at room temperature. The staining of each well,proportional to the concentration of GM2AP or Saposin B recognized bythe specific antibody used, is estimated by reading the absorbance.

Example 15 Assay of the GM2AP Proteins in the Urines

The GM2AP protein was assayed in the urines of 22 patients sufferingfrom multiple sclerosis (MS), 5 patients suffering from otherneurological diseases (OND) and 9 individuals chosen from the activepopulation and taken during a medical visit (healthy), according to theElisa protocol described below, using anti-GM2AP polyclonal antibodies.The MS patients selected for this study are confirmed patients, that isto say with various stages and profiles of the disease, and differenttreatments, and the like.

The results of the assay are presented in FIG. 8. Whereas only 0/5 ONDurines and 2/9 so-called “Healthy” urines have a GM2AP concentrationgreater than 200 ng/ml, 10/22 (that is 45%) have a concentration greaterthan 200 ng/ml.

These results indicate that while the GM2AP protein is present in a verylow concentration (<400 ng/ml) in the urines of individuals from theactive population, it is present in higher concentration in the urinesof MS patients. However, 12 MS urines also exhibit low levels of GM2AP.Among these 12 patients, 10 are under treatment. The high urinaryconcentrations of GM2AP appear to be a marker for the MS pathology, andmore precisely a marker for one stage or one form of the disease, forthe activity of the disease, and is certainly influenced by any ongoingtreatment. It should be noted that two individuals in the activepopulation have high GM2AP concentrations (these two cases werevoluntarily included in the study, because they both exhibited agliotoxic activity in their urines unlike the other individuals of thissame category). It is impossible to know if they are healthyindividuals, or individuals suffering from a pathological condition, orindividuals suffering from multiple sclerosis because the samples fromthe so-called “Healthy” individuals were collected anonymously, with noknowledge of their clinical file.

Higher urinary concentrations of GM2AP are detected in the urines of MSpatients; a high concentration of GM2AP can then be a marker for the MSpathology, and more precisely for one form of the disease, for one stageof the disease, or for a period of activity, and may be influenced byany ongoing treatment. These high urinary concentrations of GM2AP mayalso have a predictive value for the onset of a worsening of thedisease, or for a benign MS at the onset of a progression, and the like.

The absolute values of the GM2AP concentrations detected in the urinesare dependent on the affinity and the specificity of the antibody used,but in general, the tendency between the three groups of individuals ispreserved regardless of the antibody used.

Example 16 Assay of the Saposin B Proteins in the Urines

The Saposin B protein was detected in the same urine samples as thoseused to study the detection of GM2AP. The assays were carried out inparallel with those of GM2AP, in the same study, according to the Elisaprotocol described below, using anti-Saposin B polyclonal antibodies.

The results of the Saposin B assay are presented in FIG. 9. 0/5 ONDurines and 2/9 Healthy urines have a Saposin B concentration greaterthan 2 μg/ml, while 6/22 (that is 27%) exhibit a concentration greaterthan 2 μg/ml.

These results indicate that the Saposin B protein is present in eachurine (so-called healthy population or so-called sick population) atsignificant concentrations, that is to say <2 μg/ml. These assay resultsare compatible with those described in the literature. However, even ifSaposin B is present in each urine, it appears to be present in a higherconcentration in certain MS urines. This increase in Saposin Bconcentration in the MS urines is perhaps masked by the basalconcentration of this protein in the ordinary state. Thus, the highurinary concentrations of Saposin B appear to be a marker for the MSpathology, and more precisely a marker for one stage or one form of thedisease, or for the activity of the disease, and is certainly influencedby any ongoing treatment. The Saposin B assayed alone appears, however,to be a marker which discriminates for one form or for one activity ofthe disease slightly less than GM2AP. It should again be noted that twoindividuals from the active population have high Saposin Bconcentrations and they are the same individuals who also had a highGM2AP concentration in their urine.

In conclusion, higher urinary concentrations of Saposin B are detectedin the urines of MS patients; a high Saposin B concentration cantherefore be a marker for the MS pathology, and more precisely for oneform of the disease, for one stage of the disease, or for a period ofactivity, and may be influenced by any ongoing treatment. These highurinary GM2AP concentrations may also have a predictive value for anonset of a worsening of the disease, or for a benign MS at the beginningof a progression, and the like. However, in general, the high Saposin Bconcentrations alone appear to be markers which are less discriminatorythan high GM2AP concentrations alone.

The absolute values of the Saposin B concentrations detected in theurines are dependent on the affinity and specificity of the antibodyused, but in general, the tendency between the three groups ofindividuals is preserved regardless of the antibody used.

Example 17 Coassay of the GM2AP and Saposin B Proteins in the Urines

FIG. 10 presents the GM2AP concentrations assayed in the urine samplesdescribed in FIG. 5 relative to the Saposin B concentration assayed inthese same samples and described in FIG. 6. The MS samples (darkdiamonds) and the OND and “Healthy” samples (white diamonds) arepresented on this graph.

On this graph, it appears clearly that:

the higher the GM2AP concentration in the urines, the higher the SaposinB concentration. (We have shown that it is not a general case with otherproteins and that it does not indicate a renal disturbance, with theassay of creatinine in parallel for each of the samples tested);

the high GM2AP and Saposin B concentrations are characteristic of the MSsamples (with the exception of two urines from the active population,mentioned above). These joint high GM2AP and Saposin B concentrationsare markers for the MS pathology, more precisely for a window of thedisease (quadran on the right and at the top of the graph).

In conclusion, this analysis confirms that high urinary concentrationsof GM2AP (>400 ng/ml) and of Saposin B (>2 μg/ml) are codetected in theurines of MS patients and may represent markers for the MS pathology,more precisely for one form of the disease, for one stage of thedisease, or for a period of activity, and may be influenced by anyongoing treatment. It is advantageous to assay the two proteins inparallel in each sample, and to consider the two concentrations.

Assay of GM2AP and Saposin B in the Urine of Two Patients in the Form ofKinetics

MS Patient No. 1—Progressive Remittent Form

Urines of this patient were collected during the progression of hisdisease. The patient was hospitalized on D0 for an attack. He wassubjected on D1 to a flash of corticoids and was then monitored overtime from a clinical point of view (the flash provided clinicalimprovement). FIG. 11 shows the profile for the assay of GM2AP and ofSaposin B in these urines during the progression, and FIG. 12 shows theprofile of the product of the two GM2AP and Saposin B concentrations,indicating a codetection of high concentrations. The high GM2AP andSaposin B concentrations at the time of the attack and hospitalizationdecrease gradually over time after the flash of corticoids up to 90days.

MS Patient No. 2—Progressive Form

Urines of this patient were collected during the progression of hisdisease. The patient was hospitalized on D0 for an attack. He wassubjected on D1 to a flash of Endoxan and was then monitored over timefrom a clinical point of view (the flash provided clinical improvementand at D60, signs of a worsening of the disease were observed). FIG. 13shows the profile for the assay of GM2AP and of Saposin B in theseurines during the progression, and FIG. 14 shows the profile of theproduct of the two GM2AP and Saposin B concentrations, indicating acodetection of high concentrations. The high GM2AP and Saposin Bconcentrations at the time of the attack and hospitalization decreasegradually over time after the flash of Endoxan (also calledcyclophosphamide) up to 23 days and appear to increase, becoming high atD60, thus showing a perfect correlation with the progression of theclinical signs.

These results confirm that:

high concentrations of GM2AP and Saposin B in the urines are markers forthe MS pathology, and in particular the codetection of highconcentrations of the two proteins together (indicated by the product ofthe two concentrations);

the high concentrations of GM2AP and Saposin B in the urines are markersfor the activity of the disease (here during the attack) or are markersinfluenced by the immunosuppressive treatments such as corticoids andEndoxan which lower the concentrations.

This example illustrates the fact that these markers can be used, interalia:

to carry out a therapeutic monitoring of a patient and evaluate thetherapeutic benefits of a treatment for a given patient; or

to predict a worsening of the disease, predict an activity peak, and thelike

to decide on an anticipated therapeutic resumption based on the clinicalsigns

Example 18 Correlation Between the Detection of the MRP14, GM2AP andSaposin B Proteins in the Urines and the Gliotoxicity Measured in theseUrines

To verify a correlation between the presence of these proteins alone orin combination in the urines and the gliotoxicity of the urines, theconcentrations of a protein of interest and the gliotoxicity of a sampleof urines from patients suffering from multiple sclerosis (MS), frompatients suffering from other neurological diseases (OND) and fromindividuals taken from the active population termed “Healthy” wereassayed in parallel. Among the MS patients, patients are noted withvarious forms and stages of the disease, under treatment or otherwise,at various activities of the disease.

The MRP, GM2AP and Saposin B proteins were assayed in human urinesaccording to the Elisa protocols described above. The assays analyzed inthis example are those described in the preceding examples. Each urinesample analyzed in Elisa was analyzed by the MTT test to measure thegliotoxicity of each sample. The gliotoxicity is expressed as apercentage of dead cells (estimated by colorimetry using tetrazoliumsalts) of a murine astrocyte cell line (CLTT1.1) after 48 hours ofincubation in the presence of centrifuged urine.

FIG. 15 represents the GM2AP concentration as a function of thegliotoxicity of the urines determined by the MTT test.

22 MS urines (gray diamonds), 5 OND urines (black diamonds) and 9so-called “Healthy” urines (black diamonds) were presented on the graph.They are the same urines which were studied in examples 15 and 16. It isobserved that all the control urines (OND and Healthy) have low levelsof GM2AP (<400 ng/ml) and a low gliotoxicity (<15%), with the exceptionof a Healthy control urine (already commented upon in example 15) forwhich a high GM2AP concentration and gliotoxicity are observed.

The MS urines are divided into three subpopulations:

urines with low GM2AP concentration (<400 ng/ml) and low gliotoxicity(<15%),

urines with low GM2AP concentration (<400 ng/ml) and gliotoxicity(>15%), that is essentially 3 urines,

urines at high GM2AP concentration (>400 ng/ml) and high gliotoxicity(>15%).

These three subpopulations perhaps indicate MS subpopulations, that isto say different forms or stages of the disease, different activities ofthe disease, different therapeutic benefits, and the like.

However, it can be noted that all the urines having a high GM2APconcentration also have a high gliotoxicity.

In conclusion, a correlation is observed between high urinary GM2APconcentration and gliotoxicity (all the urines with a high GM2APconcentration are gliotoxic (10/10), and all the urines with a low GM2APconcentration are not gliotoxic (<15%), with the exception of 3urines/12 MS). This indicates the involvement of the GM2AP protein inthe mechanism of gliotoxicity, alone or in combination, in its naturalor modified form, but which is recognizable by an anti-GM2AP antibody.Furthermore, the codetection of a high GM2AP concentration in the urinesand of a high gliotoxicity correlates with one subpopulation of patientssuffering from MS.

FIG. 16 represents the Saposin B concentration as a function of thegliotoxicity of the urines determined by the MTT test.

22 MS urines (gray diamonds), 5 OND urines (black diamonds) and 9so-called “Healthy” urines (light gray diamonds) were presented on thegraph. They are the same urines which were studied in examples 15 and16. It is observed that the richer the urines are in Saposin B, the moregliotoxic they are. There is a fairly clear correlation between theSaposin B concentration and the gliotoxicity of the urines.

In conclusion: a correlation is observed between high urinary Saposin Bconcentration and gliotoxicity. This indicates involvement of theSaposin B protein in the mechanism of gliotoxicity, alone or incombination, in its natural or modified form, but which is recognizableby the anti-Saposin B antibody used for the assay.

FIG. 17 represents the product of the GM2AP and Saposin B concentrationsas a function of the gliotoxicity of the urines determined by the MTTtest.

The 22 MS urines (gray diamonds), 5 OND urines (black diamonds) and 9so-called “Healthy” urines (light gray diamonds) of examples 15 and 16were presented in FIG. 17. The gliotoxicity of these urines is analyzedaccording to the product of the GM2AP and Saposin B concentrations, thatis to say according to the codetection of the two proteins in theurines. A correlation is very clearly observed between the product ofthe two GM2AP and Saposin B concentrations and the gliotoxicity which ismuch higher than on considering only one protein. It is observed that5/5 of the OND urines have a low product of GM2AP and Saposin Bconcentration and a low gliotoxicity; 8/9 “Healthy” urines have a lowproduct of GM2AP and Saposin B concentration and/or a low gliotoxicity.On the other hand, essentially three subpopulations of MS urines aredistinguished:

urines at low GM2AP.Saposin B concentration and low gliotoxicity (<15%),

urines at high GM2AP.Saposin B concentration and high gliotoxicity(>15%).

These two subpopulations perhaps indicate MS subpopulations, that is tosay different forms or stages of the disease, different activities ofthe disease, different therapeutic benefits and the like. However, it isvery important to note that all the urines having a high GM2AP andSaposin B concentration, that is to say having simultaneously a highGM2AP and Saposin B concentration, also have a high gliotoxicity. Thetwo subpopulations of MS patients are all the more marked and clear whenthe three markers are considered together: gliotoxicity, high GM2APconcentration and high Saposin B concentration. This is confirmed inFIG. 18.

In conclusion: a correlation is observed between high urinary GM2AP andSaposin B concentration and gliotoxicity. All the urines with a highGM2AP and Saposin B concentration are gliotoxic, and all the urines witha low GM2AP and Saposin B concentration are not gliotoxic (<15%), withthe exception of 2 urines/22 MS. This indicates the involvement of thetwo proteins GM2AP and Saposin together or in combination in themechanism of gliotoxicity, in their natural or modified form, but whichis recognizable by the anti-GM2AP and anti-Saposin B antibodies used forthe assay. Furthermore, the codetection of a high urinary GM2AP andSaposin B concentration and of a high gliotoxicity correlates with asubpopulation of patients suffering from MS (stage, form, activity,treatment of the disease?), compared with another subpopulation. Thesethree markers considered together make it possible to discriminatebetween two subpopulations of MS patients.

Variation of the gliotoxicity and of the GM2AP and Saposin Bconcentrations as a function of the progression of the disease in twopatients after and during treatment

The correlation between gliotoxicity, high GM2AP and Saposinconcentration in the urines and MS pathology was also confirmed bymeasuring these three parameters in the urine of two patients during theprogression of their disease.

Patient No. 1: MS remittent-progressive form, hospitalized on D0 for anattack and who had received a flash of corticoid on D1. After the flash,he showed a clinical improvement up to D90—(cf. FIGS. 11, 12), PatientNo. 2: MS progressive form, hospitalized on D0 for an attack and havingreceived a flash of Endoxan (also called cyclophosphamide) on D1. OnD60, he shows new clinical signs of a worsening of his disease—(cf.FIGS. 13, 14).

The following were shown for the two patients:

a correlation between the urinary gliotoxicity and the clinicalprogression of the disease (when the clinical signs are severe, thegliotoxicity is high; when the clinical signs decrease following thetreatment, the gliotoxicity decreases and becomes stationary; when thesigns of a worsening appear after the treatment, the gliotoxicityappears to increase again),

a correlation between the gliotoxicity level in the urines of patientsand the GM2AP and Saposin B concentrations, and

a correlation between the high GM2AP and Saposin B concentrations andthe clinical progression of the disease.

In conclusion: the assay of the GM2AP and Saposin B proteins in theurines is a good discriminatory marker for a subpopulation of MS (stage,form, activity, treatment of the disease). The GM2AP and/or Saposin Bproteins are involved in the mechanism of gliotoxicity, alone or incombination, in their natural form or in a form which is recognizable bythe polyclonal antibodies used for their assay. As the GM2AP and SaposinB proteins are codetected in high concentration in the gliotoxic urines,it is possible that these two proteins act in combination to induce thegliotoxicity.

Example 19 Immunohistochemical Analysis of the Expression of the GM2A,SAPB, MRP14 and MRP8 Proteins in a Culture System Producing Gliotoxin InVitro (Monocyte Cultures), and in Normal and Pathological CerebralTissue for MS and for Controls

Protocol: Cultures of monocytes from a patient suffering from MS andfrom a healthy control were carried out in parallel, according to thepresent protocol described briefly. Starting with peripheral blood fromthese two volunteers collected over ACD, the PBMC (Peripheral BloodMononuclear Cells) are isolated on Ficoll using the technique known topersons skilled in the art. The cells recovered (at the level of thering) are washed twice in RPMI medium. The cells are then counted onKovas slide and are inoculated in a primary bottle of 25 cm² or onLabteck slide (8 wells) (in permanox) in RPMI medium supplemented with15% human AB serum on D0. The cells are cultured on “Labtek” typechamber slides in order to obtain a direct support for the analysis ofthe monocytes which adhere to the support and subsequently differentiateinto macrophages. For the slides, 2×10⁶ cells are then inoculated in anamount of 0.25×10⁶ cells/well. For the bottles, 4×10⁶ cells areinoculated in an amount of 0.25×10⁶ cells/well. On D1, the cells insuspension are recovered and the Labteck wells or the bottles are washedtwice with RPMI (previously heated to 37° C.) before adding RPMI mediumsupplemented with 5% human AB serum. On D1, D3, D6, D9, D12 or 14, D15,the culture medium is changed; the supernatants are collected and thecells bound to the slides using the techniques known to persons skilledin the art. At each change of medium, at least two slides were fixed inparaformaldehyde and stored for the immunohistochemical analysis.

Composition of the medium: RPMI (500 ml) with 15 ml of 200 mM glutamate,5 ml 100 μM sodium pyruvate, 5 ml of nonessential amino acids (100×),antibiotics penicillin and streptomycin 100 000 U/μl and anti-humaninterferon antibodies at 100 U/μl.

Results: Four cultures of monocytes in vitro were thus studied in theform of kinetics: two cultures of monocytes derived from blood fromcontrol individuals and two cultures of monocytes derived from MSpatients. At various culture times (D0, D1, D3, D6, D9, D12, was), thecorresponding supernatants were also recovered. Once the kinetics wascompleted, the slides corresponding to the different days of culturewere incubated in the presence of anti-GM2A, SAP-B, MRP-8 and MRP14polyclonal antibodies. The gliotoxicity of each supernatant thusrecovered was estimated by the MTT test. The concentration of GM2AP,MRP14 and Saposin B protein was also determined in each supernatant bythe Elisa protocol as described in examples 13 and 14.

The immunofluorescence results on fixed cells are summarized below; itis possible to note:

an absence of expression of MRP8 at all the stages of the 2 cultures

a clear expression of MRP-14 in the period between D9 and D15, found inthe two cultures, although higher in the MS culture. This expressionappears to correlate with a macrophage differentiation stage.

a very low expression (low intensity and low number of cells) isobserved at the beginning of the culture in the control culture andprobably corresponds to the physiological presence of GM2A in themacrophage lysosomes.

In the MS culture, a much more marked expression of GM2A (greaterintensity and larger number of cells) is observed, with a relativelyhomogeneous cytoplasmic labeling between D3 and D6, disappears on D9 andis again noted on D14–D15 with an intense labeling localized at thecytoplasmic periphery, defining the inner contour of the plasmamembrane. These observations are not found in all the control slides.

Analysis with the anti-SAP-B antibody did not make it possible to obtainan interpretable immunohistochemical labeling.

In the MS monocyte cultures already carried out, 3/3 had a gliotoxicitypeak at D9 and 2/3 a smaller peak at D6, no peak being detected in thecultures of monocytes of 2/2 non-MS controls analyzed in parallel.Likewise, the assay of the MRP14, GM2AP and Saposin B proteins in thesupernatant of the cell cultures during the kinetics showed that theSapB and GM2AP proteins are detected by Elisa in the supernatants of theMS monocytes and not in those of the control monocytes, on days D6 andespecially D9 of the culture; the proteins are not detected beyond thiskinetic. It should be noted that the antibodies used for the assay canrecognize the physiological forms of the proteins, but also thecomplexed and/or modified forms.

It is therefore observed that the period D6–D9 during which the highestgliotoxicity is observed in the supernatant is covered by the periodD3–D15 during which a less differentiated production of the negativecontrol for GM2A is observed in the cells with quantitative andqualitative fluctuations of its cellular expression (quantity ofexpression and cellular localization).

Example 20 Immunohistological Technique on Brain Sections in Paraffin

The histological sections prepared in paraffin are made paraffin free inxylene and alcohol before undergoing a pretreatment intended to unmaskthe antigens; this pretreatment may correspond to (i) twice 5 minutesunder microwave (750W) in the presence of a sodium citrate, citric acidbuffer, (ii) a treatment with acid by incubating for 15 minutes in a 1%periodic acid solution or by incubating for 5 minutes in a 99% formicacid solution. The endogenous peroxidases are then blocked by incubatingthe slides for 30 minutes in 1% hydrogen peroxide, followed by extensivewashing in water for 15 minutes. The background noise is blocked byincubating the slides for 30 minutes in the presence of PBS-0.03%Triton, 10% Donkey serum (for the polyclonal antibodies) or 10% Goatserum (for the monoclonal antibodies). Labeling with the primaryantibody is carried out by applying 100 to 200 μl of primary antibodysolution per slide (0.5 to 5 μg/ml according to the titer) in PBS-0.03%Triton and then incubating for 2 hours at room temperature. The slidesare then rinsed 3 times in PBS-Triton for 10 minutes. Secondary antibodylabeling is carried out using biotinylated antibodies capable of bindingspecifically to the primary antibodies, for example anti-rabbit IgG oranti-mouse IgG antibodies diluted in PBS-0.03% Triton. The slides arewashed and incubated in a solution for 2 hours (2 μlstreptavidin-biotin-peroxide complex, 1 600 μl PBS-0.03% Triton). Theslides are again washed before being revealed, protected from light, inbuffer A and then rinsed with water before microscope observation.Buffer A for 5 slides: 25 ml 0.05M Tris, pH 7.6, 2.5 ml 1M Imidazole, 15ml sterile water, 2 ml DAB 5 mg/ml, 5 ml 10% ammonium nickel, 30 μl 1%H₂O₂.

The same antibodies were used for an immunohistochemical study,according to the technique briefly described below, on paraffined slidesobtained by microtome section of brain collected post mortem from MS andfrom controls who had died from non-neurological pathologies.

The results of the analysis are summarized below:

There is no labeling of the “non-MS” and MS brains in the “normal”(non-lesioned) white substance and gray substance with the differentanti-MRP8, MRP14 and GM2A antibodies. A nonspecific reactivity did notmake it possible to interpret the results with the anti-saposin Bantibody in this immunohistochemical application.

On the other hand, the following are noted in the plaque zones of MSbrains:

an anti-MRP14 reactivity in the macrophage and microglial cells, havinga relatively homogeneous distribution over the entire stretch of thedemyelination zones (plaques),

a lower (less frequent) anti-MRP8 reactivity essentially linked toperivascular lymphoid infiltrates

a clear anti-GM2A reactivity in the macrophages and microgliocytes ofthe plaque zones, with a particular density in the zones constitutingthe “glial wall” at the peripheral limit of a plaque. Labeling of a fewastrocytes was also observed in the demyelination zones.

These different observations show that there is a particularhyperexpression of MRP-14 and GM2A proteins in the cultures of MSmonocytes producing a gliotoxic activity in their supernatant, as wellas in the zones defining demyelination plaques in the MS brains. Theytherefore reflect the reality of the coincidence between their abnormalcoexpression, the production of gliotoxic activity and the demyelinationlesions.

Furthermore, their abnormal production in the context of MS, inmacrophage blood cells as well as in those of the brain, indicates thatit is justified to carry out their assay in biological fluids tocorrelate their quantity with the lesional and inflammatory activity ofMS.

Example 21 Measurement of the Activity of the T Cells by Proliferationof the T Cells (Sredni et al., 1981).

The T cells are washed twice in culture medium in order to remove anytrace of IL2 present in the initial culture medium. B lymphocytes(EBV-LCL) or monocytes/macrophages taken as antigen-presenting cells areirradiated at 10 000 rads, and washed twice with culture medium (RPMI).2×10⁴ T cells (2×10⁵ cells/ml) and 2×10⁴ irradiated autologous B cells(2×10⁵ cells/ml) are incubated together in the presence of an increasingantigen concentration range in a final volume of 200 μl in microwells.After 48 hours of culture at 37° C., 1 μCi of 3H-thymidine in 50 μl ofRPMI medium is added to each well. The T cells, the only cells whichdivide, incorporate the tritiated thymidine into the DNA. After 18 hoursof culture, the cells of each microwell are harvested on glass woolpastilles by aspiration. After osmotic lysis of the cells, theradioactivity incorporated into the DNA is absorbed onto the pastilles(cell Harvester 530, Inotech). Each dried pastille is placed in aplastic tube which contains 2 ml of scintillant; the radioactivity badsorbed on each of the pastilles is quantified in a liquidscintillation beta counter (LKB Rackbeta 1217). The results areexpressed as an arithmetic mean of cpm/culture (“counts per minute”).

Example 22 Protocol for Detecting the Association Between the Peptidesand the Histocompatibility Molecules (Approach APC Transformed with aPeptide Binding to MHC I).

1) Materials:

The sources of histocompatibility molecules are currently of two maintypes: mutant cells and purified histocompatibility molecules.

The mutant cell used is the human T2 cell which and a variant of the T1line produced by fusion of the CEM T lymphoma and of the 721.174 Blymphoma (Salter and Cresswell Embo J 1986, 5: 943–949). This cell,which lacks peptide transporters, contains heavy chains of class Imolecules free of peptides which will be able to accept exogenouspeptides.

Class I histocompatibility molecules purified by affinity chromatographyfrom human B cell lines transformed with EBV can also be used. In thiscase, the endogenous peptides should be removed by a treatment with 1.5M urea and 12.5 mM sodium hydroxide (pH 11.7) for 1 hour at 4° C.,followed by their removal by a desalting column (PDLO, Pharmacia). Thehisto-compatibility molecules are immediately placed in contact with thepeptides to be tested in a PBS buffer with 0.05% Tween 20, 2 mM EDTA,0.1% NP40 and 6 mM CHAPS, in the presence of 2 μg/ml B2m to facilitatereassociation (Gnjatic et al., Eur J Immunol 1995 25: 1638–1642).

The peptides tested have in general 8 to 10 residues, sometimes 11 or12. They were synthesized by Néosystems (Strasbourg), or by Chironmimotopes (Victoria, Australia). They are used at concentrations varyingfrom 100 μM to 0.1 nM.

2) Protocol for assembly (Connan et al., Eur J Immunol 1994, 24: 777;Couillin et al. Eur J Immunol 1995, 25: 728–732).

Aliquots of 8.105 cells in a volume of 64 μl, distributed in Eppendorfmicrofuge tubes, are brought into contact with a lysis buffer containing10 mM PBS, pH 7.5, 1% NP40, protease inhibitors (1 mM PMSF, 100 μMiodoacetamide, 2 μg/ml aprotinin, 10 μM leupeptin, 10 μM pepstatin and10 μg/ml trypsin inhibitor). The lysis is performed in the presence ofthe peptides to be tested for 30 minutes or 1 hour at 37° C. Afterremoving the nonsolubilized material by centrifugation at 15 000revolutions/minute at 4° C., the supernatant and supplemented with 140μl of PBS containing 0.05% Tween 20, 3 mM of sodium azide, 1 mM PMSF and10 mg/ml of bovine albumin. Each sample is incubated for 20 hours at 4°C. in 2 wells of a microtiter plate of the Nunc type, Maxisorb,previously coated with a monoclonal antibody (10 μg/ml in PBS) whichrecognizes the histocompatibility molecules having conformingconformation(s) for the presentation of peptides and similar to that(those) present at the surface of the cells. The antibody-coated plateis saturated beforehand with bovine albumin at 10 mg/ml in PBS-Tweenbefore placing the sample. The second antibody which allows thedetection of the assembly of the histo-compatibility molecules isdirected against B2m. It is coupled either to biotin (NHS-LC biotin,Pierce) or to alkaline phosphatase (P-552, Sigma) and is incubated at 2μg/ml for one hour at 37° C. In the case of the use of biotin, anincubation of 45 minutes at 20–25° C. with streptavidin coupled toalkaline phosphatase (E-2636, Sigma) is carried out. The activity ofalkaline phosphatase is measured using, as substrate,4-methyl-umbelliferyl phosphate (M-8883, Sigma) at 100 μM in 50 mMdiethanolamine, pH 9.5 with 1 mM MgCl₂. The reading is carried out at340/460 nm with the aid of a cytofluorimeter.

3) Stability of the HLA/peptide complexes:

The stability of the abovementioned complexes was studied because itdetermines the good presentation of the antigen and the induction of theT response. To this effect, either purified HLA or the T2 cell lysatewas used. With purified HLA, the endogenous peptides were removed (asdescribed in 2)) and then it was brought into contact with the peptideto be tested in an Eppendorf tube at 37° C., for periods varying from afew minutes to several days. The following incubation phase on a 96-wellplate (as described in 2) with the anti-HLA antibody is performed forone hour at 37° C. The revealing is carried out in a conventionalmanner. With the T2 cell lysate, all the incubations are also carriedout at 37° C., after addition of all the protease inhibitors.

1. A polypeptide comprising at least one fragment of SEQ ID NO: 9, saidfragment comprising at least one of SEQ ID NO: 68 or SEQ ID NO:
 72. 2.The polypeptide as claimed in claim 1, characterized in that itcomprises SEQ ID NO:
 9. 3. The polypeptide as claimed in claim 1,characterized in that it consists of SEQ ID NO:
 9. 4. A method fordetecting at least one ligand associated with multiple sclerosis, in abiological sample, characterized in that the biological sample isbrought into contact with at least one polypeptide as defined in claim1, and then the formation of a complex between said polypeptide and theligand is detected.
 5. The method as claimed in claim 4, characterizedin that the biological sample is in addition brought into contact withat least one polypeptide comprising at least one fragment of a proteinchosen from proteins whose peptide sequence in the native state isselected from the group consisting of SEQ ID NO: 1 to SEQ ID NO: 8 andSEQ ID NO: 10 to SEQ ID NO: 29 and peptide sequences which exhibit atleast 70% identity with any one of SEQ ID NO: 1 to SEQ ID NO: 8 and SEQID NO: 10 to SEQ ID NO:
 29. 6. The method as claimed in claim 4,characterized in that said ligand is an antibody, a receptor, asubstrate for enzymatic activity or an enzyme for which said polypeptideis a cofactor.
 7. The method as claimed in claim 4, characterized inthat the biological sample is urine, cerebrospinal fluid or serum.
 8. Amethod for detecting at least one polypeptide as defined in claim 1, ina biological sample, characterized in that the biological sample isbrought into contact with at least one ligand that specifically binds tosaid polypeptide, and then the formation of a complex between saidpolypeptide and said ligand is detected, wherein said ligand is selectedfrom the group consisting of an antibody, a substrate with enzymaticactivity, an enzyme for which said polypeptide is a cofactor and areceptor.
 9. The method as claimed in claim 8, characterized in that thebiological sample is urine, cerebrospinal fluid or serum.
 10. Anucleotide fragment, characterized in that it encodes a polypeptide asdefined in claim 1.